clusters clusters-00 clusters-01 dist-perres energies fluctuation hbonds interactions pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 1AK4

PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns

Omid Mokhtari
Hamed Khakzad
Yasaman Karami

Delta team, Inria center at the University of Lorraine

Peptidyl-prolyl cis-trans isomerase A, N-terminally processed

Interaction with human PPIA/CYPA and NUP153

Dimerization/Multimerization of capsid protein p24

Cis/trans isomerization of proline peptide bond; by human PPIA/CYPA


Dynarepo 1AKJ

HLA class I histocompatibility antigen, A alpha chain

T-cell surface glycoprotein CD8 alpha chain


Dynarepo 1AVA

Alpha-amylase type B isozyme
Transition state stabilizer
Alpha-amylase/subtilisin inhibitor
Disordered
Reactive bond


Dynarepo 1B6C

Peptidyl-prolyl cis-trans isomerase FKBP1A


Dynarepo 1BVN

Pancreatic alpha-amylase
Transition state stabilizer
Alpha-amylase inhibitor HOE-467A


Dynarepo 1DFJ

Ribonuclease pancreatic
Ribonuclease inhibitor


Dynarepo 1DP5

Saccharopepsin
Peptidase A1
Protease A inhibitor 3
Inhibitory domain
Disordered


Dynarepo 1E96

Ras-related C3 botulinum toxin substrate 1


clusters clusters-00 clusters-01 clusters-02 clusters-03 dist-perres energies fluctuation hbonds interactions pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 1EER

Erythropoietin
Erythropoietin receptor
Fibronectin type-III
WSXWS motif
Required for ligand binding


Dynarepo 1EMV

Colicin-E9 immunity protein
Colicin-E9
Disordered


Dynarepo 1EWY

Ferredoxin--NADP reductase
FAD-binding FR-type
Disordered
Ferredoxin-1
2Fe-2S ferredoxin-type


Dynarepo 1F3V

Tumor necrosis factor receptor type 1-associated DEATH domain protein


Dynarepo 1FC2

Immunoglobulin G-binding protein A
Immunoglobulin heavy constant gamma 1
Ig-like 2
Ig-like 3
CH2
CH3


Dynarepo 1FFW

Chemotaxis protein CheY
Response regulatory
Chemotaxis protein CheA


clusters clusters-00 clusters-01 clusters-02 clusters-03 clusters-04 clusters-05 dist-perres energies fluctuation hbonds interactions pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 1FLT

Vascular endothelial growth factor A, long form

Vascular endothelial growth factor receptor 1


Dynarepo 1FSK

Major pollen allergen Bet v 1-A
Immunoglobulin kappa constant
Ig-like
Ig heavy chain Mem5
Ig-like 1
Ig-like 2
D segment
JH2 segment


clusters clusters-00 clusters-01 clusters-02 clusters-03 dist-perres energies fluctuation hbonds interactions pca rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 1GCQ

Growth factor receptor-bound protein 2
SH3 2
Proto-oncogene vav
SH3 1


Dynarepo 1GO4

Mitotic spindle assembly checkpoint protein MAD2A

Required for assuming the closed conformation and for interaction with CDC20

Mitotic spindle assembly checkpoint protein MAD1


Dynarepo 1GPW

Imidazole glycerol phosphate synthase subunit HisF

Imidazole glycerol phosphate synthase subunit HisH


Dynarepo 1GUA

RAF proto-oncogene serine/threonine-protein kinase


Dynarepo 1I51

Caspase-7 subunit p20
Caspase-7 subunit p11
Loop L1
Loop L2
Loop L3
Loop L4
Involved in allosteric regulation
E3 ubiquitin-protein ligase XIAP
Interaction with caspase-7


Dynarepo 1I5K

Plasminogen-binding group A streptococcal M-like protein PAM


Dynarepo 1I8L

Important for interaction with CD80 and CD86


clusters clusters-00 clusters-01 clusters-02 clusters-03 clusters-04 clusters-05 clusters-06 dist-perres energies fluctuation hbonds interactions pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 1IB1

Interaction with phosphoserine on interacting protein

Important for the catalytic mechanism; involved in substrate deprotonation


Dynarepo 1ICF

HLA class II histocompatibility antigen gamma chain


Dynarepo 1J7D

Ubiquitin-conjugating enzyme E2 variant 2


Dynarepo 1JWH

Casein kinase II subunit alpha
Protein kinase
Interaction with beta subunit
Casein kinase II subunit beta
Interaction with alpha subunit
KSSR motif


Dynarepo 1K5D

GTP-binding nuclear protein Ran
Interaction with RANBP1
Essential for GTP hydrolysis
Ran-specific GTPase-activating protein
RanBD1
Disordered
Ran GTPase-activating protein 1
Disordered
Critical residue for GTP hydrolysis


Dynarepo 1KAC

Fiber protein
Coxsackievirus and adenovirus receptor
Ig-like C2-type 1
Ig-like C2-type 2


Dynarepo 1KGY

Classical MD simulations, 3 replicates of 500 ns

Author Omid Mokhtari
Author Hamed Khakzad
Author Yasaman Karami

Ephrin type-B receptor 2
Eph LBD
Ephrin-B2
Ephrin RBD


Dynarepo 1L2W

Outer membrane virulence protein YopE
Disordered


Dynarepo 1LFD

Ral guanine nucleotide dissociation stimulator


clusters clusters-00 clusters-01 clusters-02 clusters-03 clusters-04 clusters-05 dist-perres energies fluctuation hbonds interactions pca rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 1LJ2

Eukaryotic translation initiation factor 4 gamma 1


Dynarepo 1LX5

Bone morphogenetic protein 7
Activin receptor type-2A


Dynarepo 1LZW

ATP-dependent Clp protease adapter protein ClpS

ATP-dependent Clp protease ATP-binding subunit ClpA


Dynarepo 1M10

VWFA 1; binding site for platelet glycoprotein Ib


Dynarepo 1MQ8

Intercellular adhesion molecule 1
Ig-like C2-type 1
Ig-like C2-type 2
Cell attachment site; atypical
Integrin alpha-L
VWFA


Dynarepo 1MTN

Chymotrypsin A chain A
Chymotrypsin A chain B
Chymotrypsin A chain C
Peptidase S1
Pancreatic trypsin inhibitor
BPTI/Kunitz inhibitor
Reactive bond for trypsin


Dynarepo 1MXE

Calcium/calmodulin-dependent protein kinase type 1


Dynarepo 1OQE

Tumor necrosis factor ligand superfamily member 13b, membrane form

Tumor necrosis factor ligand superfamily member 13b, soluble form

Tumor necrosis factor receptor superfamily member 13C

Essential for TNFSF13B/TALL1/BAFF/BLyS binding


Dynarepo 1P27

Protein mago nashi homolog
RNA-binding protein 8A
RRM
Disordered


Dynarepo 1PK1

Polyhomeotic-proximal chromatin protein
SAM
Polycomb protein Scm
SAM


Dynarepo 1PVH

Interleukin-6 receptor subunit beta
Fibronectin type-III 1
Fibronectin type-III 2
WSXWS motif
Leukemia inhibitory factor


Dynarepo 1PXV

Staphopain B
Cleavage; by SspA
Staphostatin B
Binds to staphopain B


Dynarepo 1QA9

Lymphocyte function-associated antigen 3


Dynarepo 1RLB

Transthyretin
Retinol-binding protein 4
Plasma retinol-binding protein(1-182)
Plasma retinol-binding protein(1-181)
Plasma retinol-binding protein(1-179)
Plasma retinol-binding protein(1-176)


Dynarepo 1RVJ

Reaction center protein L chain
Reaction center protein M chain
Reaction center protein H chain


Dynarepo 1RY7

Fibroblast growth factor 1
Heparin-binding
Nuclear localization signal
Fibroblast growth factor receptor 3
Ig-like C2-type 2
Ig-like C2-type 3
Disordered


Dynarepo 1S1Q

Tumor susceptibility gene 101 protein
UEV
Ubiquitin
Ubiquitin-like 1
Interacts with activating enzyme
Essential for function


Dynarepo 1SYQ

Vinculin
N-terminal globular head
Talin-interaction
3 X 112 AA tandem repeats
Talin-1
Helical bundle R1


Dynarepo 1T63

Interaction with coactivator LXXL and FXXFY motifs

Interaction with coactivator FXXLF and FXXFY motifs


Dynarepo 1TA3

Xylanase inhibitor protein 1
GH18
Interaction with fungal GH11 xylanase
Interaction with fungal GH10 xylanase
Endo-1,4-beta-xylanase C
GH10


Dynarepo 1TDQ

Tenascin-R
Fibronectin type-III 2
Fibronectin type-III 3
Fibronectin type-III 4
Fibronectin type-III 5
Aggrecan core protein
C-type lectin
Disordered
G3


Dynarepo 1TE1

Interaction with protein inhibitor XIP-I


Dynarepo 1U0S

Chemotaxis protein CheY
Response regulatory
Chemotaxis protein CheA


Dynarepo 1UEX

VWFA 1; binding site for platelet glycoprotein Ib


mem-map clusters clusters-00 clusters-01 dist-perres energies fluctuation hbonds interactions pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 1UGH

Uracil-DNA glycosylase
Uracil-DNA glycosylase inhibitor


Dynarepo 1UUZ

Inhibitor of vertebrate lysozyme
Important for lysozyme inhibition
Lysozyme C
C-type lysozyme


Dynarepo 1V7P

Snaclec EMS16 subunit alpha
C-type lectin
Key residue for binding with integrin
Snaclec EMS16 subunit beta
C-type lectin
Key residue for binding with integrin
Integrin alpha-2
VWFA


Dynarepo 1VET

Ragulator complex protein LAMTOR3
Required for interaction with LAMTOR2
Ragulator complex protein LAMTOR2
Required for location at endosomes


Dynarepo 1WQJ

Insulin-like growth factor-binding protein 4


Dynarepo 1WR6

ADP-ribosylation factor-binding protein GGA3


Dynarepo 1WRD

Target of Myb1 membrane trafficking protein


Dynarepo 1WVE

4-cresol dehydrogenase [hydroxylating] flavoprotein subunit

4-cresol dehydrogenase [hydroxylating] cytochrome c subunit


Dynarepo 1X75

DNA gyrase subunit A
Topo IIA-type catalytic
Toxin CcdB


Dynarepo 1XD3

Ubiquitin carboxyl-terminal hydrolase isozyme L3

Interaction with ubiquitin. Crossover loop which restricts access of large ubiquitin adducts to the active site


mem-map clusters clusters-00 clusters-01 dist-perres energies fluctuation hbonds interactions pca rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 1XG2

Pectinesterase 1
Transition state stabilizer
Pectinesterase inhibitor


Dynarepo 1XQS

Hsp70-binding protein 1
Heat shock 70 kDa protein 1A
Nucleotide-binding domain (NBD)


Dynarepo 1XWD

Glycoprotein hormones alpha chain
Follitropin subunit beta
Follicle-stimulating hormone receptor
LRRNT


Dynarepo 1YCS

Cellular tumor antigen p53
Interaction with CCAR2
Disordered
Interaction with WWOX
Interaction with HIPK1
Required for interaction with ZNF385A
Required for interaction with FBXO42
Interaction with AXIN1
Interaction with the 53BP2 SH3 domain
Interaction with E4F1
Interaction with DNA
Apoptosis-stimulating of p53 protein 2
SH3
Mediates interaction with APC2


Dynarepo 2AW2

Tumor necrosis factor receptor superfamily member 14


Dynarepo 2BDN

Involved in dimerization, receptor binding and signaling

Involved in GAG binding and receptor binding

Variable (V) domain, involved in antigen recognition


clusters clusters-00 clusters-01 clusters-02 clusters-03 clusters-04 dist-perres energies fluctuation hbonds interactions pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 2BO9

Carboxypeptidase A4
Peptidase M14
Latexin
Cystatin LXN-type 1
Cystatin LXN-type 2
Alpha-helical linker


Dynarepo 2BP7

2-oxoisovalerate dehydrogenase subunit alpha

2-oxoisovalerate dehydrogenase subunit beta


Dynarepo 2BYK

Chromatin accessibility complex 16kD protein


clusters clusters-00 clusters-01 dist-perres energies fluctuation hbonds interactions pca rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 2C7N

Rab5 GDP/GTP exchange factor
Interaction with ubiquitinated proteins
Disordered
Ubiquitin
Ubiquitin-like 2


Dynarepo 2CJS

Regulating synaptic membrane exocytosis protein 2


Dynarepo 2D10

Na(+)/H(+) exchange regulatory cofactor NHE-RF1


Dynarepo 2F4M

UV excision repair protein RAD23 homolog B


Dynarepo 2G45

Ubiquitin carboxyl-terminal hydrolase 5
Ubiquitin
Ubiquitin-like 9


Dynarepo 2G9H

HLA class II histocompatibility antigen, DR alpha chain

Self- and pathogen-derived peptide antigen

HLA class II histocompatibility antigen, DRB1 beta chain


Dynarepo 2GH0

Artemin
Disordered
GDNF family receptor alpha-3


Dynarepo 2HEV

Tumor necrosis factor ligand superfamily member 4

Tumor necrosis factor receptor superfamily member 4


Dynarepo 2HRK

Interaction with methionyl-tRNA synthetase MES1

Interaction with glutamyl-tRNA synthetase GUS1


Dynarepo 2HTH

Vacuolar protein-sorting-associated protein 36


Dynarepo 2HWN

cAMP-dependent protein kinase type II-alpha regulatory subunit


Dynarepo 2I32

Interaction with histone H3, CHAF1B, and HIRA

Required for repression of histone gene transcription


Dynarepo 2IFF

Variable (V) domain, involved in antigen recognition


Dynarepo 2IY0

(Microbial infection) Interaction with Tula hantavirus


Dynarepo 2IYB

Protein enabled homolog
WH1
Testin
LIM zinc-binding 2
LIM zinc-binding 3


Dynarepo 2J0T

Interstitial collagenase
22 kDa interstitial collagenase
Metalloprotease
Not glycosylated
Metalloproteinase inhibitor 1
NTR
Involved in metalloproteinase-binding


Dynarepo 2J8S

Multidrug efflux pump subunit AcrB
GA-binding protein subunit beta-1


Dynarepo 2JIX

Ig-like domain-containing protein
Ig-like
Erythropoietin receptor
Fibronectin type-III
WSXWS motif
Required for ligand binding
Ig-like


Dynarepo 2JJT

Tyrosine-protein phosphatase non-receptor type substrate 1


Dynarepo 2JKI

Histidine kinase/HSP90-like ATPase
Disordered
Protein SGT1 homolog A
CS


Dynarepo 2NQD

Chagasin
BC loop
DE loop
FG loop
Cathepsin L
Cathepsin L heavy chain
Cathepsin L light chain
Cleavage; by autolysis


Dynarepo 2OIN

Genome polyprotein
Serine protease/helicase NS3
Non-structural protein 4A
Peptidase S29
Protease NS2-3
NS3-binding


Dynarepo 2OJE

HLA class II histocompatibility antigen, DR alpha chain

Self- and pathogen-derived peptide antigen

HLA class II histocompatibility antigen, DRB1 beta chain


Dynarepo 2OMY

Internalin A
LRRNT
LRRCT
Cadherin-1
Cadherin 1


Dynarepo 2PCB

Cytochrome c peroxidase, mitochondrial
Transition state stabilizer
Cytochrome c


Dynarepo 2PJY

Transforming growth factor beta-3
TGF-beta receptor type-2
TGF-beta receptor type-1


Dynarepo 2PSM

Interleukin-15
Interleukin-15 receptor subunit alpha
Sushi


Dynarepo 2PTT

CD48 antigen
Ig-like C2-type 1
Natural killer cell receptor 2B4
Ig-like 1


Dynarepo 2Q0O

Probable transcriptional activator protein TraR


Dynarepo 2QEJ

Immunoglobulin heavy constant alpha 1
Ig-like 2
Ig-like 3
Disordered
Staphylococcal superantigen-like 7


Dynarepo 2QHO

Ubiquitin
Ubiquitin-like 2
E3 ubiquitin-protein ligase UBR5
UBA


Dynarepo 2QXV

Interaction with DNMT1, DNMT3A and DNMT3B


Dynarepo 2SNI

Subtilisin BPN'
Peptidase S8
Subtilisin-chymotrypsin inhibitor-2A
Disordered
Reactive bond


Dynarepo 2UUY

Serine protease 1
Alpha-trypsin chain 1
Alpha-trypsin chain 2
Peptidase S1


Dynarepo 2V1D

Lysine-specific histone demethylase 1A
SWIRM
Disordered
Demethylase activity
REST corepressor 1
SANT 2
Disordered
Interaction with KDM1A
Histone H3.1t
Disordered


Dynarepo 2V5Q

Serine/threonine-protein kinase PLK1
Protein kinase
Activation loop
GA-binding protein subunit beta-1


Dynarepo 2V8S

Vesicle transport through interaction with t-SNAREs homolog 1B


Dynarepo 2W80

Complement factor H
Sushi 5
Sushi 6
Sushi 7
Factor H binding protein
Domain A
Domain B
Domain C
Important for antibody recognition


Dynarepo 2W8B

Tol-Pal system protein TolB
TolA box
Peptidoglycan-associated lipoprotein
OmpA-like


Dynarepo 2WD5

Structural maintenance of chromosomes protein 1A

Structural maintenance of chromosomes protein 3


Dynarepo 2WO3

Ephrin type-A receptor 4
Eph LBD
Ephrin-A2
Ephrin RBD


Dynarepo 2WP0

Chromosomal replication initiator protein DnaA

Domain I, interacts with DnaA modulators


Dynarepo 2WX0

TGF-beta-activated kinase 1 and MAP3K7-binding protein 2


Dynarepo 2X89

Beta-2-microglobulin
Beta-2-microglobulin form pI 5.3
Ig-like C1-type


Dynarepo 2X9A

Attachment protein G3P
Disordered
Disordered


Dynarepo 2XBB

E3 ubiquitin-protein ligase NEDD4
HECT
Mediates interaction with TNIK
Ubiquitin
Ubiquitin-like
Interacts with activating enzyme
Essential for function


Dynarepo 2XQR

Beta-fructofuranosidase, insoluble isoenzyme CWINV1


Dynarepo 2XZE

Intramolecular interaction with N-terminus


Dynarepo 2YGG

Necessary and sufficient for interaction with PCP4


clusters clusters-00 clusters-01 clusters-02 dist-perres energies fluctuation hbonds interactions pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 2YVJ

FAD/NAD(P)-binding
Reductase C-terminal
Biphenyl dioxygenase ferredoxin subunit
Rieske


Dynarepo 2ZXX

Necessary and sufficient for interaction with IDAS and CDT1


Dynarepo 3B08

RanBP-type and C3HC4-type zinc finger-containing protein 1


Dynarepo 3BH6

ADP-ribosylation factor-like protein 3
Protein XRP2
C-CAP/cofactor C-like


Dynarepo 3BIK

Programmed cell death 1 ligand 1
Ig-like V-type
Ig-like C2-type
Programmed cell death protein 1
Ig-like V-type
Interaction with CD274/PDCD1L1


Dynarepo 3C5T

Interaction with the endogenous ligand GLP-1


Dynarepo 3C66

Poly(A) polymerase
Disordered
Interaction with RNA
Pre-mRNA polyadenylation factor FIP1
Disordered


Dynarepo 3C9A

Protein giant-lens
Protein spitz
EGF-like


Dynarepo 3CQX

BAG family molecular chaperone regulator 2


clusters clusters-00 fluctuation pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 3D5O

Low affinity immunoglobulin gamma Fc region receptor II-a


Dynarepo 3DGC

Interleukin-22
Interleukin-22 receptor subunit alpha-1
Fibronectin type-III 1
Fibronectin type-III 2


Dynarepo 3DXC

Amyloid beta precursor protein binding family B member 1

Required for the interaction with KIF5B and for anterograde transport in axons

YENPXY motif; contains endocytosis signal


Dynarepo 3E2U

CAP-Gly domain-containing linker protein 1


Dynarepo 3EGG

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit


Dynarepo 3EJH

Fibronectin
Fibronectin type-I 8
Fibronectin type-I 9
Collagen-binding
Collagen alpha-1(I) chain
Disordered
Triple-helical region


Dynarepo 3EOY

Outer capsid protein sigma-1
Tail
Head
Junctional adhesion molecule A
Ig-like V-type 1


Dynarepo 3F1P

Endothelial PAS domain-containing protein 1

Aryl hydrocarbon receptor nuclear translocator


Dynarepo 3F4Y

Envelope glycoprotein gp160
Transmembrane protein gp41
Immunosuppression
MPER; binding to GalCer


mem-map clusters clusters-00 clusters-01 clusters-02 clusters-03 clusters-04 dist-perres energies fluctuation hbonds interactions pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 3FF8

Killer cell lectin-like receptor subfamily G member 1


Dynarepo 3FXD

Endothelin-converting enzyme 2
Peptidase M13
IcmR middle region


Dynarepo 3G9W

Signal for sorting from recycling endosomes; interaction with ACAP1


Dynarepo 3GJ8

GTP-binding nuclear protein Ran
Essential for GTP hydrolysis
Nuclear pore complex protein Nup153
29 X 2 AA repeats of F-G


Dynarepo 3GS2

Required for cellular lifespan extension


Dynarepo 3GTY

Trigger factor
PPIase FKBP-type
Small ribosomal subunit protein uS7


Dynarepo 3H7B

HLA class I histocompatibility antigen, A alpha chain


mem-map clusters clusters-00 clusters-01 clusters-02 clusters-03 clusters-04 clusters-05 clusters-06 dist-perres energies fluctuation hbonds interactions pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 3H8D

Interaction with TAX1BP1 and CALCOCO2/NDP52

Sufficient for interaction with SH3KBP1 SH3 domain


Dynarepo 3HAE

Variable (V) domain, involved in antigen recognition


Dynarepo 3HG0

Receptor-binding protein of phage tail base-plate Siphoviridae head


Dynarepo 3HPW

Toxin CcdB
Antitoxin CcdA
Interaction with DNA
Interaction with CcdB


Dynarepo 3HTU

Vacuolar protein-sorting-associated protein 25


Dynarepo 3HUG

ECF RNA polymerase sigma factor SigL
Sigma-70 factor domain-4
Anti-sigma-L factor RslA


Dynarepo 3IA3

(Microbial infection) Cleavage; by N.americanus apr-2


Dynarepo 3IT8

Tumor necrosis factor, membrane form
Tumor necrosis factor, soluble form
THD
Ig-like


Dynarepo 3K1R

Harmonin
PDZ 1
N-terminal domain
pre-mRNA splicing regulator USH1G
SAM


Dynarepo 3K2M

Tyrosine-protein kinase ABL1
SH3
SH2
Fibronectin
Fibronectin type-III 10
Fibronectin type-III 11
Fibronectin type-III 12
Cell-attachment
Cell attachment site


Dynarepo 3K6G

Telomeric repeat-binding factor 2-interacting protein 1


Dynarepo 3K75

DNA repair protein XRCC1
DNA polymerase beta
DNA-binding


Dynarepo 3K9M

Cathepsin B
Cathepsin B light chain
Cathepsin B heavy chain
Cystatin-A
Cystatin-A, N-terminally processed
Secondary area of contact
Reactive site


Dynarepo 3KNB

Titin
Ig-like 152
Obscurin-like protein 1
Ig-like 1
Interaction with TTN


Dynarepo 3KXF

HLA class I histocompatibility antigen, B alpha chain


Dynarepo 3LK2

F-actin-capping protein subunit beta isoforms 1 and 2


Dynarepo 3NVQ

Semaphorin-7A
Sema
Ig-like C2-type
Interaction with integrins
Cell attachment site
Plexin-C1
Sema


mem-map clusters clusters-00 clusters-01 clusters-02 clusters-03 dist-perres energies fluctuation hbonds interactions pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 3O4O

Involved in interaction with TMED10 C-terminus

Interleukin-1 receptor type 2, membrane form

Interleukin-1 receptor accessory protein


Dynarepo 3O6Q

Stage II sporulation protein SA
Stage II sporulation protein SB


Dynarepo 3OAK

Transcription factor SPN1
TFIIS N-terminal
Transcription elongation factor SPT6


Dynarepo 3OGO

Variable (V) domain, involved in antigen recognition


Dynarepo 3ONA

Chemokine and involved in interaction with ITGAV:ITGB3 and ITGA4:ITGB1


Dynarepo 3ONW

Guanine nucleotide-binding protein G(i) subunit alpha-1


Dynarepo 3OWT

DNA-binding protein RAP1
Activation domain
Regulatory protein SIR3


Dynarepo 3P8M

General control transcription factor GCN4


Dynarepo 3P9W

Vascular endothelial growth factor A, long form


Dynarepo 3QBT

Inositol polyphosphate 5-phosphatase OCRL


Dynarepo 3QHT

Ubiquitin-like protein SMT3
Ubiquitin-like
Fibronectin
Fibronectin type-III 10
Fibronectin type-III 11
Cell-attachment
Cell attachment site


Dynarepo 3QQ8

Transitional endoplasmic reticulum ATPase

RMSD check has failed: there may be sudden jumps along the trajectory


Dynarepo 3QT2

Interleukin-5 receptor subunit alpha
Fibronectin type-III 1
Fibronectin type-III 2
WSXWS motif
Interleukin-5
Not glycosylated


Dynarepo 3QWQ

Epidermal growth factor receptor
Fibronectin
Fibronectin type-III 10
Fibronectin type-III 11
Fibronectin type-III 12
Cell-attachment
Cell attachment site


Dynarepo 3RZW

(Microbial infection) Interaction with Tula hantavirus


Dynarepo 3S5L

HLA class II histocompatibility antigen, DR alpha chain

Self- and pathogen-derived peptide antigen

HLA class II histocompatibility antigen, DRB1 beta chain


Dynarepo 3SSB

Inducible metalloproteinase inhibitor protein


Dynarepo 3SYN

Flagellar biosynthesis protein FlhF
Flagellum site-determining protein YlxH


Dynarepo 3U82

Envelope glycoprotein D
Interaction with TNFRSF14
Profusion
Disordered
Nectin-1
Ig-like V-type
Ig-like C2-type 1
Ig-like C2-type 2
Interaction with FGFR


Dynarepo 3UL4

Receptor binding site for duplicated segment of CipA


Dynarepo 3UYO

Tyrosine-protein kinase ABL1
SH3
SH2
Fibronectin
Fibronectin type-III 10
Fibronectin type-III 11
Cell-attachment
Cell attachment site


Dynarepo 3UZ0

Stage III sporulation protein AH
Stage II sporulation protein Q


Dynarepo 3VEP

Anti-sigma-D factor RsdA
Interaction with sigma factor
ECF RNA polymerase sigma factor SigD
Sigma-70 factor domain-4


Dynarepo 3VUX

Tumor necrosis factor alpha-induced protein 3

Sufficient for inhibitory activity of TNF-induced NF-kappa-B activity

Required for lysosomal localization and for TRAF2 lysosomal degradation


Dynarepo 3VYS

PurM-like N-terminal
PurM-like C-terminal


Dynarepo 3VZA

Interaction with the N-terminus of SPBC24

Interaction with the C-terminus of SPBC24


Dynarepo 3WA0

Merlin
FERM
DDB1- and CUL4-associated factor 1
Disordered
Interaction with NF2


Dynarepo 3WWQ

Fanconi anemia core complex-associated protein 20


Dynarepo 3ZRZ

Fibronectin
Fibronectin type-I 2
Fibronectin type-I 3
Fibrin- and heparin-binding 1
Required for binding to LILRB4


Dynarepo 3ZU7

Mitogen-activated protein kinase 1
Protein kinase
TXY
GA-binding protein subunit beta-1


Dynarepo 3ZWH

Protein S100-A4
EF-hand 1
EF-hand 2
Myosin-9
Disordered


Dynarepo 1DE4

Transferrin receptor protein 1, serum form

Cell attachment site; required for binding to transferrin


Dynarepo 4AOQ

Serine protease 1
Alpha-trypsin chain 1
Alpha-trypsin chain 2
Peptidase S1
Reactive bond for trypsin


Dynarepo 4AQE

Cadherin-23
Cadherin 1
Cadherin 2
Protocadherin-15
Cadherin 1
Cadherin 2


Dynarepo 4AYE

Complement factor H
Sushi 5
Sushi 6
Sushi 7
Factor H binding protein
Domain A
Domain B
Domain C
Important for antibody recognition


Dynarepo 4AYI

Factor H binding protein-like C-terminal


Dynarepo 4BQD

Tissue factor pathway inhibitor
BPTI/Kunitz inhibitor 1
BPTI/Kunitz inhibitor 2
Reactive bond


Dynarepo 4BRU

ATP-dependent RNA helicase DHH1
Helicase ATP-binding
Helicase C-terminal
Q motif
DEAD box
Enhancer of mRNA-decapping protein 3
DFDF
Disordered


Dynarepo 4BWQ

Thioredoxin-like protein 4A
Polyglutamine-binding protein 1
Disordered
Important for interaction with TXNL4A


Dynarepo 4C1N

CO dehydrogenase/acetyl-CoA synthase delta subunit TIM barrel


Dynarepo 4CC4

Internalin C
Dynamin-binding protein
SH3 6


Dynarepo 4CJ2

Lysozyme C
C-type lysozyme
DNA-binding protein 7d
DNA-binding protein 7a
DNA-binding protein 7b


Dynarepo 4D2G

Proliferating cell nuclear antigen
Interaction with NUDT15
PCNA-associated factor
Disordered
PIP-box


Dynarepo 4DBG

RanBP-type and C3HC4-type zinc finger-containing protein 1


Dynarepo 4DCN

ADP-ribosylation factor-like protein 1
Arfaptin-2
AH


Dynarepo 4DVG

Ras-like GTP-binding protein RHO1
Switch 1
Switch 2
GBD/FH3


Dynarepo 4EEF

Hemagglutinin
Hemagglutinin HA1 chain
Hemagglutinin HA2 chain
Cleavage; by host
Transcription factor RADIALIS
SANT


Dynarepo 4EOZ

Speckle-type POZ protein
BTB
Required for nuclear localization
Important for homodimerization
Cullin-3
Interaction with KLHL18


Dynarepo 4EQA

Peptidoglycan amidase Tse1
Immune protein Tsi1


Dynarepo 4ETW

Pimeloyl-[acyl-carrier protein] methyl ester esterase


Dynarepo 4EXP

Macrophage colony-stimulating factor 1 receptor


Dynarepo 4FAO

Growth/differentiation factor 2
Interaction with ENG
Activin receptor type-1-like
Mediates specificity for BMP ligand
Activin receptor type-2B


Dynarepo 4FQ0

Flagellar motor switch protein FliG
Part of the EHPQR-motif


Dynarepo 4G8A

Toll-like receptor 4
LRRCT
Lymphocyte antigen 96
Interaction with lipopolysaccharide


Dynarepo 4GEQ

Interacts with the NDC80 complex subunits SPC24 and SPC25 and with the KNL1 complex


Dynarepo 4GN4

Aspartate--tRNA(Asp) ligase
Important for tRNA discrimination
Lysozyme C
C-type lysozyme


Dynarepo 4H2W

Amino acid--[acyl-carrier-protein] ligase 1


Dynarepo 4H5S

Cytotoxic and regulatory T-cell molecule


Dynarepo 4HEP

Receptor-binding protein of phage tail base-plate Siphoviridae head


Dynarepo 4IHH

Involved in determining the hydroxyacyl-ACP selectivity


Dynarepo 4ILW

Metalloproteinase inhibitor 2
NTR
Involved in metalloproteinase-binding
Stromelysin-2


Dynarepo 4J2L

Ataxin-1
AXH
Self-association
Interaction with USP7
RNA-binding
Protein capicua homolog
Interaction with ATXN1


Dynarepo 4JW3

Neocarzinostatin
Phycocyanobilin lyase subunit alpha


Dynarepo 4K1R

AMSH-like protease sst2
MPN
JAMM motif
Indirect zinc-binding
Ubiquitin
Ubiquitin-like 1
Ubiquitin-like 2
Interacts with activating enzyme
Essential for function


Dynarepo 4KR0

Dipeptidyl peptidase 4 membrane form
Dipeptidyl peptidase 4 soluble form
BetaCoV S1-CTD


Dynarepo 4LLO

Voltage-gated delayed rectifier potassium channel KCNH1

Interaction with cyclic nucleotide-binding pocket


Dynarepo 4LRX

PEP-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK

PTS-dependent dihydroxyacetone kinase operon regulatory protein


Dynarepo 4LRZ

PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL


Dynarepo 4LYL

Uracil-DNA glycosylase-like
Uracil-DNA glycosylase inhibitor


Dynarepo 4LZX

Necessary and sufficient for interaction with PCP4


Dynarepo 4M0W

Replicase polyprotein 1a
Papain-like protease nsp3
Ubiquitin-like 2
Peptidase C16
Ubiquitin
Ubiquitin-like
Disordered
Interacts with activating enzyme
Essential for function


Dynarepo 4M5F

Peptidoglycan muramidase Tse3
Immune protein Tsi3
Disordered


Dynarepo 4MP0

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

Serine/threonine-protein phosphatase 1 regulatory subunit 10


Dynarepo 4MQV

Interaction with RAD52, TIPIN, UNG and XPA

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1


Dynarepo 4MRT

Tyrocidine synthase 3
Carrier 3
Domain 3 (tyrosine-activating)
4'-phosphopantetheinyl transferase Sfp
Peptidyl carrier protein binding


Dynarepo 4N7V

Serine/threonine-protein kinase PLK4
Cryptic POLO box 1 (CPB1)
Cryptic POLO box 2 (CPB2)
Centrosomal protein of 152 kDa
Interaction with PLK4
Disordered


Dynarepo 4NG2

Transcriptional activator protein LasR
LasR-specific antiactivator QslA


Dynarepo 4NIQ

Vacuolar protein sorting-associated protein 4


Dynarepo 4NL9

Ankyrin repeat and SAM domain-containing protein 3

Ankyrin repeat and SAM domain-containing protein 6


Dynarepo 4NSO

Type VI secretion system spike protein VgrG3


Dynarepo 4PW9

Moybdenum cofactor oxidoreductase dimerisation


Dynarepo 4Q5E

Protein kinase OspG
Ubiquitin
Ubiquitin-like 1
Ubiquitin-conjugating enzyme E2 L3
UBC core


Dynarepo 4Q96

Regulation of nuclear pre-mRNA domain-containing protein 1B


Dynarepo 4QLP

Immunity factor for TNT
Outer membrane channel protein CpnT
TNT


Dynarepo 4REY

Essential for interaction with GOLGA2/GM130


Dynarepo 4U2X

Membrane-associated protein VP24
Importin subunit alpha-6
NLS binding site (minor)


Dynarepo 4UDM

Colicin E3 immunity protein
Colicin E3
Disordered
Linker
Ribosome inactivating activity
Cytotoxic RNase (C) domain
Binding of immunity protein
Stabilizes positive charge on His-513


Dynarepo 4UU9

Variable (V) domain, involved in antigen recognition


clusters clusters-00 clusters-01 clusters-02 dist-perres energies fluctuation hbonds interactions pca rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores


Dynarepo 4XKH

Ubiquitin
Ubiquitin-like 2
AN1-type zinc finger protein 2B
UIM 1
UIM 2


Dynarepo 4XL5

Green fluorescent protein
Phycocyanobilin lyase subunit alpha


Dynarepo 4XWJ

Regulator of sigma D
Interaction with RpoD
Phosphocarrier protein HPr
HPr


Dynarepo 4Y61

Receptor-type tyrosine-protein phosphatase delta

Mini-exon peptide A9; sufficient for interaction with IL1RAPL1

Mini-exon peptide B; required for interaction with SLITRK2 and in the function in pre-synaptic differentiation; Acts as an adjustable linker to control relative positions and orientations of the PTPRD second and third immunoglobilin domains for their simultaneous interactions with the first immunoglobilin domain of IL1RAPL1 and IL1RAP; Modulates affinity for IL1RAPL1 and IL1RAP


Dynarepo 4YIQ

Cell adhesion molecule CEACAM8
Ig-like V-type
Cell adhesion molecule CEACAM6
Ig-like V-type


Dynarepo 4YN0

Tumor necrosis factor receptor superfamily member 21


Dynarepo 4ZQU

Deoxyribonuclease CdiA
DNase activity
Immunity protein CdiI-YPIII


Dynarepo 4ZRK

Merlin
FERM
Serine/threonine-protein kinase LATS1
Disordered


Dynarepo 4ZW2

Voltage-dependent L-type calcium channel subunit beta-1

Voltage-dependent L-type calcium channel subunit alpha-1S


Dynarepo 5B78

Histone acetyltransferase KAT6A
Interaction with PML
Histone H2A/H2B/H3
Disordered


Dynarepo 5BXQ

Nuclear transport factor 2
NTF2
GTP-binding nuclear protein Ran
Interaction with RANBP1
Essential for GTP hydrolysis


Dynarepo 5CTR

Squamous cell carcinoma antigen recognized by T-cells 3

Necessary and sufficient for U6 snRNA binding


Dynarepo 5CX3

Microtubule-associated protein 1 light chain 3 alpha

Important for interaction with ATG13 and for autophagosome formation

FYVE and coiled-coil domain-containing protein 1


Dynarepo 5DJU

Immunoglobulin G-binding protein A
PAS
PAC


Dynarepo 5DMJ

Tumor necrosis factor receptor superfamily member 5


Dynarepo 5DOB

Nuclear egress protein 1
Disordered
Nuclear egress protein 2


Dynarepo 5E6J

Papain-like protease nsp3
Ubiquitin-like 2
Peptidase C16
Ubiquitin
Ubiquitin-like 1
Interacts with activating enzyme
Essential for function


Dynarepo 5EB1

Negative regulator YfiR
Outer-membrane lipoprotein YfiB
OmpA-like


Dynarepo 5ELU

Cysteine proteinase inhibitor
Secondary area of contact
Small ubiquitin-related modifier 2
Ubiquitin-like


Dynarepo 5F1B

Involved in receptor recognition and/or post-binding events

NPC intracellular cholesterol transporter 1


Dynarepo 5F5S

Pre-mRNA-splicing factor 38A
N-terminal protein interaction domain
Microfibrillar-associated protein 1


Dynarepo 5FZT

Helical bundle R7A; Interaction with KANK1

Helical bundle R7B; Interaction with KANK1


Dynarepo 5GJK

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Dynarepo 5IMY

Thiol-activated cytolysin C-terminal
CD59 glycoprotein
UPAR/Ly6


Dynarepo 5IP4

Ig heavy chain V-III region W3082
Ig-like
Neuronal migration protein doublecortin
Doublecortin 2


Dynarepo 5IUS

Programmed cell death protein 1
Ig-like V-type
Nivolumab binding
Interaction with CD274/PDCD1L1
Pembrolizumab binding
Programmed cell death 1 ligand 1
Ig-like V-type
Ig-like C2-type


Dynarepo 5J4A

Probable inner membrane translocation domain

C-terminal effector domain (CT), has tRNA nuclease activity


Dynarepo 5J7C

Lysozyme C
C-type lysozyme
Fibronectin
Fibronectin type-III 10
Fibronectin type-III 11
Fibronectin type-III 12
Cell-attachment
Cell attachment site


Dynarepo 5JDO

(Microbial infection) Cleavage; by N.americanus apr-2


Dynarepo 5JEM

Interferon regulatory factor 3
Mediates interaction with ZDHHC11
Interaction with HERC5
CREB-binding protein


Dynarepo 5JJD

Ceramide transfer protein
PH
START
Disordered


Dynarepo 5JZE

Involved in the ligation of specific target proteins


Dynarepo 5KWY

NPC intracellular cholesterol transporter 2


Dynarepo 5KY5

GDP-fucose protein O-fucosyltransferase 1


Dynarepo 5L21

N-terminus of receptor binding domain (N-RBD)

C-terminus of receptor binding domain (C-RBD)


Dynarepo 5LXQ

Protein tyrosine phosphatase type IVA 1
Tyrosine-protein phosphatase
Interaction with ATF5
Metal transporter CNNM2
CNNM transmembrane
CBS 1
CBS 2


Dynarepo 5MJY

Tyrosine-protein phosphatase non-receptor type 23

Zinc finger FYVE domain-containing protein 9


Dynarepo 5ML9

Low affinity immunoglobulin gamma Fc region receptor III-A


Dynarepo 5OTJ

Variable (V) domain, involved in antigen recognition


Dynarepo 5OYL

Spike glycoprotein fusion
Spike glycoprotein G central
Low-density lipoprotein receptor
LDL-receptor class A 1
LDL-receptor class A 2


Dynarepo 5SXP

Rho guanine nucleotide exchange factor 7

E3 ubiquitin-protein ligase Itchy homolog


Dynarepo 5TGH

Sorting nexin-5
PX
Interaction with DOCK1


Dynarepo 5TVQ

Interaction with 5' end of substrate DNA


Dynarepo 5UK5

Neurogenic locus notch homolog protein 1


Dynarepo 5UN7

Adrenocortical dysplasia protein homolog


Dynarepo 5UPK

Cell division control protein 42 homolog


Dynarepo 5UZU

89 kDa myeloperoxidase
84 kDa myeloperoxidase
Myeloperoxidase
Myeloperoxidase light chain
Myeloperoxidase heavy chain
Transition state stabilizer


Dynarepo 5W9A

Required for interaction with GABARAP and for autophagy

Microtubule-associated protein 1 light chain 3 beta


Dynarepo 5WB7

Epidermal growth factor receptor
Proepiregulin
Epiregulin
EGF-like


Dynarepo 5WQL

Lipoprotein NlpI
Tail-specific protease
PDZ
Disordered


Dynarepo 5XQZ

MOB kinase activator 1A
Serine/threonine-protein kinase 38-like
S100B binding


Dynarepo 5Y1Z

MYND-type zinc finger-containing chromatin reader ZMYND8

Required for interaction with histone H3 and histone H4


Dynarepo 5YIR

Gamma-aminobutyric acid receptor-associated protein

Interaction with LIR (LC3 nteracting Region) motif of ATG3


Dynarepo 5Z7L

Calcium-binding and coiled-coil domain-containing protein 2


Dynarepo 6A6I

Ubiquitin
Ubiquitin-like 1
Interacts with activating enzyme
Essential for function


Dynarepo 6A7V

Ribonuclease VapC11
PINc
Antitoxin VapB11


Dynarepo 6B6U

Pyruvate kinase PKM
Interaction with POU5F1
Intersubunit contact
Transition state stabilizer
Crucial for phosphotyrosine binding


Dynarepo 6BB4

Variable (V) domain, involved in antigen recognition


Dynarepo 6BX5

Fibronectin
Fibronectin type-III 10
Fibronectin type-III 11
Cell-attachment
Cell attachment site


Dynarepo 6C48

Protein lin-9 homolog
Myb-related protein B
Protein lin-52 homolog


Dynarepo 6CO2

Interaction with dimethylated histone H4


Dynarepo 6D13

Could be important to modulate the pK values of the two catalytic cysteine residues


Dynarepo 6DNQ

Disordered
Transcriptional activator Myb
Transcriptional activation domain
Histone lysine acetyltransferase CREBBP
KIX


Dynarepo 6F3Z

Lipoprotein-releasing system transmembrane protein LolC

Outer-membrane lipoprotein carrier protein


Dynarepo 6FC3

Eukaryotic translation initiation factor 4E


Dynarepo 6FG8

Leucine-rich repeat receptor-like protein kinase binding

Probable inactive receptor kinase At1g27190


Dynarepo 6FGO

Immunoglobulin gamma-1 heavy chain
Ig-like 3
Ig-like 4
Constant (C) domain
Protein A Ig-binding
Disordered


Dynarepo 6FHP

Dispase autolysis-inducing protein
Thermolysin


Dynarepo 6FTO

Chromo domain-containing protein 2
Chromatin remodeling factor mit1


Dynarepo 6FUB

AVR-Pik-like HMA interaction
Disease resistance protein Pikm1-TS
HMA
Structured coiled coil (CC) domain
HMA-like domain


Dynarepo 6GHO

Global transcriptional regulator Spx
CXXC
ClpXP adapter protein SpxH


Dynarepo 6H9N

Cell division protein FtsQ
POTRA
Disordered
Cell division protein FtsB
Leucine zipper-like


Dynarepo 6HUL

Tryptophan synthase alpha chain
Tryptophan synthase beta chain 1


Dynarepo 6IM9

Sufficient to promote the mitochondrial pathway of apoptosis


Dynarepo 6IVZ

Envelope glycoprotein E central and dimerisation

Variable (V) domain, involved in antigen recognition


Dynarepo 6J4S

Tubulinyl-Tyr carboxypeptidase 2
Disordered
Small vasohibin-binding protein
Disordered


Dynarepo 6J9L

CRISPR-associated endonuclease Cas9
RuvC-I
ARM


Dynarepo 6JCS

Dyslexia-associated protein KIAA0319-like protein


Dynarepo 6JHW

CRISPR-associated endonuclease Cas9
HNH Cas9-type


Dynarepo 6JWJ

Nuclear protein localization protein 4
MPN
Ubiquitin fusion degradation protein 1


Dynarepo 6NZU

Iron-sulfur cluster assembly enzyme ISCU

Mediates ISCU dimerization and de novo [2Fe-2S] cluster assembly


Dynarepo 6ON9

Zwei Ig domain protein zig-8
Ig-like C2-type 1
Ig-like


Dynarepo 2AZE

Domain C; mediates interaction with E4F1


Dynarepo 4JO6

Streptavidin
Avidin-like
Cell attachment site; atypical


mem-map clusters clusters-00 clusters-01 clusters-02 dist-perres energies fluctuation hbonds interactions pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores


Dynarepo 4MP0

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit


Dynarepo 1F6M

PPIs from test53, Classical MD simulations, 3 replicates of 500 ns

Thioredoxin reductase
Thioredoxin 1
Thioredoxin
Deprotonates C-terminal active site Cys
Contributes to redox potential value


Dynarepo 1I2M

GTP-binding nuclear protein Ran
Small GTPase Ran-type
Switch-I
Switch-II
Essential for GTP hydrolysis
Regulator of chromosome condensation
Disordered
Bipartite nuclear localization signal


Dynarepo 1W1W

Structural maintenance of chromosomes protein 1


Dynarepo 1WDW

Tryptophan synthase alpha chain
Tryptophan synthase beta chain 1


Dynarepo 1ZHH

Autoinducer 2-binding periplasmic protein LuxP

Autoinducer 2 sensor kinase/phosphatase LuxQ


Dynarepo 2AYO

Ubiquitin carboxyl-terminal hydrolase 14


Dynarepo 2C0L

Peroxisomal targeting signal 1 receptor
Sterol carrier protein 2
SCP2
Microbody targeting signal


Dynarepo 2I3T

Spindle assembly checkpoint protein BUB3

Spindle assembly checkpoint component MAD3


Dynarepo 2PMS

Critical for glycosaminoglycan, lipid A, lysozyme and DNA binding

Important for full bactericidal and antifungal activities


Dynarepo 2QXV

Interaction with DNMT1, DNMT3A and DNMT3B


Dynarepo 2V3B

Rubredoxin-NAD(+) reductase
Rubredoxin-2
Rubredoxin-like


Dynarepo 2V9T

Roundabout homolog 1
Ig-like C2-type 1
Slit homolog 2 protein
Slit homolog 2 protein N-product
LRRNT 2
LRRCT 2


Dynarepo 2XWT

Variable (V) domain, involved in antigen recognition


Dynarepo 2Y5B

Ubiquitin carboxyl-terminal hydrolase 21


Dynarepo 3FHC

Nuclear pore complex protein Nup214
Seven-bladed beta propeller
44 X 2 AA repeats of F-G
ATP-dependent RNA helicase DDX19B
Helicase ATP-binding
N-terminal lobe
Q motif
DEAD box


Dynarepo 3H6G

Glutamate receptor ionotropic, kainate 2


Dynarepo 3NVN

Semaphorin-like protein 139
Sema
Plexin-C1
Sema


Dynarepo 3QML

Endoplasmic reticulum chaperone BiP
Nucleotide-binding (NBD)
Substrate-binding (SBD)
Nucleotide exchange factor SIL1


Dynarepo 3RT0

Protein phosphatase 2C 16
PPM-type phosphatase
Lock
Abscisic acid receptor PYL10
START-like
Gate loop
Latch loop
Involved in ABA binding
Involved in interactions with PP2Cs


Dynarepo 3WN7

Nuclear factor erythroid 2-related factor 2


Dynarepo 3ZWL

Eukaryotic translation initiation factor 3 subunit I

Eukaryotic translation initiation factor 3 subunit B


Dynarepo 4BKX

Metastasis-associated protein MTA1
ELM2
SANT
Histone deacetylase 1
Histone deacetylase


Dynarepo 4C9B

Eukaryotic initiation factor 4A-III, N-terminally processed


Dynarepo 4ETP

Spindle pole body-associated protein VIK1


DynaRepo 1KX5

Classical MD simulations, 6 replicas of 2000 ns

Author Yasaman Karami
Author Emmanuelle Bignon

Laboratoire de Physique et Chimie Theoriques

Karami, Y., & Bignon, E. (2024). Cysteine hyperoxidation rewires communication pathways in the nucleosome and destabilizes the dyad. Computational and Structural Biotechnology Journal, 23, 1387-1396, doi https://doi.org/10.1016/j.csbj.2024.03.025

DynaRepo Acknowledgements HPC resources IDRIS under the allocation 2022-A0120713412 made by GENCI and the Explor computing center (Grant 2019CPMXX0983)

Histone H3.2
Disordered
Histone H4
Disordered
Histone H2A type 1
Disordered
Histone H2B 1.1
Disordered

First 1 frames may be not equilibrated


First 1 frames may be not equilibrated


Dynarepo 4FZV

Transcription termination factor 4, mitochondrial

mTERF domain-containing protein 2 processed


Dynarepo 4M0W

Replicase polyprotein 1a
Papain-like protease nsp3
Ubiquitin-like 2
Peptidase C16
Ubiquitin
Ubiquitin-like
Disordered
Interacts with activating enzyme
Essential for function


Dynarepo 4X33

Diphthamide biosynthesis protein 3
DPH-type MB
Protein KTI13


Dynarepo 4YEB

Leucine-rich repeat transmembrane protein FLRT3


Dynarepo 4ZGY

Stacks against the aromatic ring of pyridoxal phosphate and stabilizes reaction intermediates


Dynarepo 4HDO

Krev interaction trapped protein 1
FERM
Interaction with RAP1B
Ras-related protein Rap-1b
Interaction with KRIT1
Effector region


Dynarepo 5TIH

Variable (V) domain, involved in antigen recognition


mem-map clusters clusters-00 fluctuation pca pockets rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 1EWY

single chains from test53, Classical MD simulations, 3 replicates of 500 ns

Ferredoxin--NADP reductase
FAD-binding FR-type
Disordered


Dynarepo 1I2M

Regulator of chromosome condensation
Disordered
Bipartite nuclear localization signal


Dynarepo 1NCA

Neuraminidase
Hypervariable stalk region
Head of neuraminidase


Dynarepo 1W1W

Structural maintenance of chromosomes protein 1


Dynarepo 1XG2

Pectinesterase 1
Transition state stabilizer


Dynarepo 1ZHH

Autoinducer 2-binding periplasmic protein LuxP


Dynarepo 2AYO

Ubiquitin carboxyl-terminal hydrolase 14


Dynarepo 2I3T

Spindle assembly checkpoint protein BUB3


Dynarepo 2PMS

Critical for glycosaminoglycan, lipid A, lysozyme and DNA binding

Important for full bactericidal and antifungal activities


Dynarepo 2V9T

Slit homolog 2 protein
Slit homolog 2 protein N-product
LRRNT 2
LRRCT 2


Dynarepo 2Y5B

Ubiquitin carboxyl-terminal hydrolase 21


Dynarepo 3FHC

Nuclear pore complex protein Nup214
Seven-bladed beta propeller
44 X 2 AA repeats of F-G


Dynarepo 3H6G

Glutamate receptor ionotropic, kainate 2


Dynarepo 3RT0

Protein phosphatase 2C 16
PPM-type phosphatase
Lock


Dynarepo 3WN7

Kelch-like ECH-associated protein 1
Sensor for electrophilic agents


Dynarepo 3ZWL

Eukaryotic translation initiation factor 3 subunit I


Dynarepo 4BKX

Histone deacetylase 1
Histone deacetylase


Dynarepo 4C9B

Pre-mRNA-splicing factor CWC22 homolog
MIF4G
Disordered


Dynarepo 4HDO

Krev interaction trapped protein 1
FERM
Interaction with RAP1B


Dynarepo 4M0W

Replicase polyprotein 1a
Papain-like protease nsp3
Ubiquitin-like 2
Peptidase C16


Dynarepo 4Y61

SLIT and NTRK-like protein 2
LRRCT 1
Required for interaction with PTPRD
Disordered


Dynarepo 4YEB

Adhesion G protein-coupled receptor L3
Olfactomedin-like
Interaction with FLRT3


Dynarepo 4ZGY

Stacks against the aromatic ring of pyridoxal phosphate and stabilizes reaction intermediates


Dynarepo 4ETP

Spindle pole body-associated protein VIK1


Dynarepo 5ZUF

Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns


Dynarepo 6HER

Major prion protein
Interaction with GRB2, ERI3 and SYN1


Dynarepo 6OEJ

Human immunodeficiency virus 1 envelope glycoprotein Gp120


mem-map clusters clusters-00 fluctuation pca rgyr rmsd-pairwise rmsd-perres rmsds sasa tmscores

Dynarepo 6PZ8

Spike glycoprotein
Spike protein S1
BetaCoV S1-NTD
BetaCoV S1-CTD


Dynarepo 6QB6

Induced myeloid leukemia cell differentiation protein Mcl-1


Dynarepo 6QD7

Envelope glycoprotein
Shed GP
GP2
Fusion peptide
Cleavage; by host furin


Dynarepo 6QFA

Gamma-aminobutyric acid receptor subunit beta-3


Dynarepo 6TYS

Fusion glycoprotein F0
Fusion glycoprotein F2
Fusion glycoprotein F1
Fusion peptide
Cleavage; by host


Dynarepo 6UUH

Variable (V) domain, involved in antigen recognition


Dynarepo 6VN0

Envelope glycoprotein gp160
Transmembrane protein gp41
Retroviral envelope protein GP41-like
Fusion peptide
Immunosuppression


Dynarepo 6WIZ

Hemagglutinin HA2 chain
Cleavage; by host


Dynarepo 6XC2

Receptor-binding motif; binding to human ACE2

Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide


Dynarepo 6YIO

Interleukin-2 receptor subunit alpha
Sushi 1
Sushi 2
Disordered


Dynarepo 6ZDH

Putative superantigen; may bind T-cell receptor alpha/TRAC

Putative superantigen; may bind T-cell receptor beta/TRBC1


Dynarepo 7ANQ

Proprotein convertase subtilisin/kexin type 9


Dynarepo 7DAA

Basigin
Ig-like C2-type
Ig-like V-type
Disordered


Dynarepo 7KET

Factor H binding protein
Domain A
Domain B
Domain C
Important for antibody recognition


Dynarepo 7KF0

Vascular endothelial growth factor A, long form


Dynarepo 7L5J

Calicivirus coat protein
Calicivirus coat protein C-terminal


Dynarepo 7L6V

Botulinum neurotoxin type A
Botulinum neurotoxin A light chain


Dynarepo 7LO6

Human immunodeficiency virus 1 envelope glycoprotein Gp120


Dynarepo 7LVW

Fusion glycoprotein F0
Fusion glycoprotein F2
Fusion glycoprotein F1
Fusion peptide
Cleavage; by host furin-like protease


Dynarepo 7NA9

Botulinum neurotoxin type B
Botulinum neurotoxin B light chain


Dynarepo 7NFQ

Influenza RNA polymerase PB2 CAP binding


Dynarepo 7NX0

Leukocyte tyrosine kinase receptor
Disordered


Dynarepo 7S11

T-cell surface protein tactile
Ig-like V-type 1


Dynarepo 7SHY

Immunoglobulin heavy constant epsilon
Ig-like 3
Ig-like 4


Dynarepo 7SJN

Serine protease HTRA1
PDZ
Serine protease
Involved in trimer stabilization


Dynarepo 7SOC

Receptor-binding motif; binding to human ACE2

Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide


Dynarepo 7SU0

Important for interaction with CD80 and CD86


Dynarepo 7TYV

Pre-glycoprotein polyprotein GP complex
Glycoprotein G1


Dynarepo 7VNG

Spike glycoprotein
S1
Interaction with ANPEP
Interaction with host ANPEP


Dynarepo 7VUX

Programmed cell death protein 1
Ig-like V-type
Nivolumab binding
Interaction with CD274/PDCD1L1
Pembrolizumab binding


Dynarepo 7WO5

Putative superantigen; may bind T-cell receptor alpha/TRAC

Putative superantigen; may bind T-cell receptor beta/TRBC1


Dynarepo 7Z4T

Involved in interaction with TMED10 C-terminus


Dynarepo 1DEE

Antigen from SAbDab, Classical MD simulations, 3 replicates of 500 ns


Dynarepo 1FE8

VWFA 3; main binding site for collagens type I and III


Dynarepo 1IQD

Coagulation factor VIII
Factor VIIIa light chain
F5/8 type C 2


Dynarepo 2H9G

Tumor necrosis factor receptor superfamily member 10B


Dynarepo 2R0L

Hepatocyte growth factor activator long chain


Dynarepo 2UZI

GTPase HRas
GTPase HRas, N-terminally processed
Hypervariable region
Effector region


Dynarepo 2VXQ

Pollen allergen Phl p 2
Expansin-like CBD


Dynarepo 2VXT

Interleukin-18
Cleavage; by CASP1, CASP4 and CASP5
Cleavage; by CASP3


Dynarepo 2W9E

Major prion protein
Interaction with GRB2, ERI3 and SYN1


Dynarepo 3KR3

Insulin-like growth factor II Ala-25 Del


Dynarepo 3LEV

Interaction with polymerase core subunit RpoC


Dynarepo 3MJ9

Junctional adhesion molecule-like
Ig-like V-type 1
Ig-like V-type 2


Dynarepo 3NH7

Bone morphogenetic protein receptor type-1A


Dynarepo 3RKD

Pro-secreted protein ORF2
Secreted protein ORF2
Oligomerization
Possible cleavage


Dynarepo 3SKJ

Ephrin type-A receptor 2
Eph LBD
Mediates interaction with CLDN4


Dynarepo 4AEI

Alpha-mammal toxin AaH2
LCN-type CS-alpha/beta
Key residue for Nav1.7/SCN9A site 3


Dynarepo 4DTG

Tissue factor pathway inhibitor
BPTI/Kunitz inhibitor 2
Reactive bond


Dynarepo 4HWB

Interleukin-13 receptor subunit alpha-1
Fibronectin type-III 2
Fibronectin type-III 3
WSXWS motif


Dynarepo 4J4P

Immunoglobulin heavy constant epsilon
Ig-like 2
Ig-like 3
Ig-like 4


Dynarepo 4K9E

Mast/stem cell growth factor receptor Kit


Dynarepo 4KXZ

Transforming growth factor beta-2 proprotein


Dynarepo 4LMQ

Important for integrin interaction and activation


Dynarepo 4QCI

Platelet-derived growth factor subunit B


Dynarepo 4WV1

Fibroblast growth factor receptor 2
Ig-like C2-type 2
Heparin-binding


Dynarepo 4ZPT

Spike glycoprotein
Spike protein S1
BetaCoV S1-CTD


Dynarepo 5BO1

Protein jagged-1
DSL
EGF-like 1
EGF-like 2; atypical
EGF-like 3
Important for interaction with NOTCH1


Dynarepo 5DFV

CD81 antigen
Important for interaction with integrin


Dynarepo 5IKC

Neuronal migration protein doublecortin
Doublecortin 1


Dynarepo 5JQ6

Clumping factor A
Disordered
Ligand binding A region


Dynarepo 5K59

Uncharacterized leukocidin-like protein 1


Dynarepo 5KW9

Capsid protein VP1
Soluble capsid protein
Protruding domain
P1 sub-domain 1
P2 sub-domain
P1 sub-domain 2


Dynarepo 5NMV

Tissue factor pathway inhibitor
BPTI/Kunitz inhibitor 1
Reactive bond


Dynarepo 5T5F

Factor H binding protein
Domain A
Domain B
Domain C
Important for antibody recognition


Dynarepo 5TZT

Leukocyte surface antigen CD47
Ig-like V-type


Dynarepo 5XMH

Immunoglobulin gamma-1 heavy chain
Ig-like 3
Ig-like 4
Constant (C) domain


Dynarepo 6B0G

25 kDa ookinete surface antigen
EGF-like 1; truncated
EGF-like 2
EGF-like 3
EGF-like 4


Dynarepo 6B0S

Circumsporozoite protein
TSP type-1
Disordered


Dynarepo 6BIT

Tyrosine-protein phosphatase non-receptor type substrate 1


Dynarepo 6E62

Gametocyte surface protein P45/48
6-Cys 2


Dynarepo 6IAP

Natural cytotoxicity triggering receptor 1


Dynarepo 6JHT

Genome polyprotein
Capsid protein VP3
Cleavage; by protease 3C


Dynarepo 6K0Y

Programmed cell death protein 1
Ig-like V-type
Nivolumab binding
Interaction with CD274/PDCD1L1
Pembrolizumab binding


Dynarepo 6MHR

Tumor necrosis factor receptor superfamily member 9


Dynarepo 6MLK

Erythronolide synthase EryA3
Thioesterase


Dynarepo 6PXH

Spike glycoprotein
Spike protein S1
BetaCoV S1-NTD


Dynarepo 6W7S

Could be the principal determinant of stereospecificity


Dynarepo 7C88

Programmed cell death 1 ligand 1
Ig-like V-type
Ig-like C2-type


Dynarepo 7CHZ

Involved in interaction with TMED10 C-terminus


Dynarepo 7CJ2

Important for AKT1 activation and IL8 production


Dynarepo 7DM2

Phosphate-binding protein PstS 1
Disordered


Dynarepo 7DUO

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1


Dynarepo 7E72

Angiopoietin-1 receptor
Fibronectin type-III 1
Fibronectin type-III 2
Fibronectin type-III 3


Dynarepo 7JVA

Receptor-binding motif; binding to human ACE2

Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide


Dynarepo 7KF1

Vascular endothelial growth factor A, long form


Dynarepo 7L7R

Involved in fusion with the host membrane


Dynarepo 7MMN

Fusion glycoprotein F0
Fusion glycoprotein F1
Fusion peptide
Cleavage; by host furin-like protease


Dynarepo 7SEG

Low affinity immunoglobulin gamma Fc region receptor III-A


Dynarepo 7SU1

Important for interaction with CD80 and CD86


DynaRepo 7CQC

Putative zinc metalloprotease aq_1964
PDZ
Podoplanin
Disordered


DynaRepo 1KX5_ocs

Classical MD simulations, 6 replicas of 2000 ns, nucleosome core particle with alpha-satellite DNA sequence and one S-sulfonylated H3C110

Histone H3.2
Disordered
Histone H4
Disordered
Histone H2A type 1
Disordered
Histone H2B 1.1
Disordered


DynaRepo 1KX5_csn

Classical MD simulations, 5 replicas of 2000 ns, nucleosome core particle with alpha-satellite DNA sequence and one S-nitrosylated H3C110, PDB id 1KX5

Yasaman Karami
Roy Gonzalez-Aleman
Mailys Duch
Yuya Qiu
Yani Kedjar
Emmanuelle Bignon

Karami, Y., Gonzalez-Aleman, R., Duch, M., Qiu, Y., Kedjar, Y., & Bignon, E. (2024). Histone H3 as a redox switch in the nucleosome core particle insights from molecular modeling. bioRxiv, 2024-10, doi.org/10.1101/2024.10.07.616940

DynaRepo Acknowledgements HPC resources from GENCI-IDRIS (Grant 2023-A0150714577) and EXPLOR (Grant 2019CP-MXX0983)


DynaRepo 1KX5_2ocs

Classical MD simulations, 6 replicas of 2000 ns, nucleosome core particle with alpha-satellite DNA sequence and two S-sulfonylated H3C110


DynaRepo 3LZ0

Classical MD simulations, 3 replicas of ~4000ns of a nucleosome core particle with the Widow 601 DNA sequence. Histone tails were reconstructed from the 1KX5 structure. PDB id 3LZ0

Ekaterina Smirnova
Emmanuelle Bignon
Patrick Schultz
Gabor Papai
Adam Ben Shem

Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire

Smirnova, E., Bignon, E., Schultz, P., Papai, G., & Shem, A. B. (2024). Binding to nucleosome poises human SIRT6 for histone H3 deacetylation. Elife, 12, RP87989, doi.org/10.7554/eLife.87989.5

DynaRepo Acknowledgements GENCI (HPC resources of IDRIS, allocation A0120713412) for computational resources

Histone H3
Disordered
Su(var)205 chromodomain-binding
Histone H4
Disordered
Histone H2A type 1
Disordered
Histone H2B 1.1
Disordered


DynaRepo 8OF4

Classical MD simulations, 2 replicas of ~4500ns of SIRT6 bound to a nucleosome core particle with the Widow 601 DNA sequence. Histone tails were reconstructed from the 1KX5 structure.

Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moléculaire et Cellulaire

Smirnova, E., Bignon, E., Schultz, P., Papai, G., & Shem, A. B. (2024). Binding to nucleosome poises human SIRT6 for histone H3 deacetylation. Elife, 12, RP87989, doi https://doi.org/10.7554/eLife.87989.5

NAD-dependent protein deacylase sirtuin-6

Formation of an covalent adduct with nitro-fatty acid activators