Structure of PDB 6yw6 Chain A Binding Site BS01

Receptor Information
>6yw6 Chain A (length=396) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKEVMKGVDDLDFFIG
DEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLT
EPPLNTPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTL
TGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRDREV
GIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAIS
KKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRR
PLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSKPKPIDVQV
ITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPV
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 A Residue 501 [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)		G13 T14 G15 Y16 K18 S170 G171 D172 K228 E229 G323 G324 S325 M327 F328
Binding residue
(residue number reindexed from 1)		G11 T12 G13 Y14 K16 S157 G158 D159 K215 E216 G310 G311 S312 M314 F315
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:0030030 cell projection 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:0070358 actin polymerization-dependent cell motility
GO:0071346 cellular response to type II interferon
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005885 Arp2/3 protein complex
GO:0005903 brush border
GO:0005911 cell-cell junction
GO:0005925 focal adhesion
GO:0015629 actin cytoskeleton
GO:0016020 membrane
GO:0030027 lamellipodium
GO:0035861 site of double-strand break
GO:0042995 cell projection
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6yw6, PDBe:6yw6, PDBj:6yw6
PDBsum6yw6
PubMed32661131
UniProtP61158|ARP3_HUMAN Actin-related protein 3 (Gene Name=ACTR3)

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