Structure of PDB 6yw6 Chain B Binding Site BS01

Receptor Information
>6yw6 Chain B (length=277) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVCDNGTGFVKCGYAGSNFPEHIFPAIDDMKHLWDYTFGPIQAVLTLYAQ
GLLTGVVVDSGDGVTHICPVYEGFSLPHLTRRLDIAGRDITRYLIKLLLL
RGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVLVESYTLPDG
RIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYK
HIVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPR
RKHMVFLGGAVLADIMKDKDNFWMTRQ
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain6yw6 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6yw6 Cryo-EM of human Arp2/3 complexes provides structural insights into actin nucleation modulation by ARPC5 isoforms.
Resolution4.2 Å
Binding residue
(original residue number in PDB)		G16 F17 G160 D161 K217 E218 G305 G306 S307 M309
Binding residue
(residue number reindexed from 1)		G8 F9 G61 D62 K118 E119 G206 G207 S208 M210
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003779 actin binding
GO:0005200 structural constituent of cytoskeleton
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0051015 actin filament binding
Biological Process
GO:0007163 establishment or maintenance of cell polarity
GO:0008356 asymmetric cell division
GO:0010592 positive regulation of lamellipodium assembly
GO:0016344 meiotic chromosome movement towards spindle pole
GO:0016482 cytosolic transport
GO:0030036 actin cytoskeleton organization
GO:0033206 meiotic cytokinesis
GO:0034314 Arp2/3 complex-mediated actin nucleation
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0051321 meiotic cell cycle
GO:0051653 spindle localization
GO:0060271 cilium assembly
GO:0071346 cellular response to type II interferon
GO:1905168 positive regulation of double-strand break repair via homologous recombination
GO:2001032 regulation of double-strand break repair via nonhomologous end joining
Cellular Component
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005885 Arp2/3 protein complex
GO:0005925 focal adhesion
GO:0005938 cell cortex
GO:0015629 actin cytoskeleton
GO:0016020 membrane
GO:0030478 actin cap
GO:0035578 azurophil granule lumen
GO:0035861 site of double-strand break
GO:0042995 cell projection
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6yw6, PDBe:6yw6, PDBj:6yw6
PDBsum6yw6
PubMed32661131
UniProtP61160|ARP2_HUMAN Actin-related protein 2 (Gene Name=ACTR2)

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