Structure of PDB 8v6v Chain W Binding Site BS03

Receptor Information
>8v6v Chain W (length=449) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YVKWGKLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLGYMK
HYRNIPGPHMVLVPKSTLHNWMSEFKRWVPTLRSVCLIGDKEQRAAFVRD
VLLPGEWDVCVTSYEMLIKEKSVFKKFNWRYLVIDEAHRIKNEKSKLSEI
VREFKTTNRLLLTGTPLQNNLHELWSLLNFLLPDVFNSADDFDSWFERLH
MVLRPFLLRRIKADVEKSLPPKKEVKIYVGLSKMQREWYTRILMKDIDIL
NSAGKMDKMRLLNILMQLRKCCNHPYLFDGAEPGPPYTTDMHLVTNSGKM
VVLDKLLPKLKEQGSRVLIFSQMTRVLDILEDYCMWRNYEYCRLDGQTPH
DERQDSINAYNEPNSTKFVFMLSTRAGGLGINLATADVVILYDSDWNPQV
DLQAMDRAHRIGQTKTVRVFRFITDNTVEERIVERAEMKLRLDSIVIQQ
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain8v6v Chain W Residue 1101 [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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PDB8v6v Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		Q184 G210 K211 T212 R595 I596
Binding residue
(residue number reindexed from 1)		Q11 G37 K38 T39 R410 I411
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0031491 nucleosome binding
GO:0042393 histone binding
GO:0140658 ATP-dependent chromatin remodeler activity
GO:0140751 histone octamer slider activity
Biological Process
GO:0000183 rDNA heterochromatin formation
GO:0006275 regulation of DNA replication
GO:0006281 DNA repair
GO:0006325 chromatin organization
GO:0006334 nucleosome assembly
GO:0006338 chromatin remodeling
GO:0006346 DNA methylation-dependent heterochromatin formation
GO:0006352 DNA-templated transcription initiation
GO:0006355 regulation of DNA-templated transcription
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006974 DNA damage response
GO:0016479 negative regulation of transcription by RNA polymerase I
GO:0031507 heterochromatin formation
GO:0045740 positive regulation of DNA replication
GO:0045893 positive regulation of DNA-templated transcription
GO:0045943 positive regulation of transcription by RNA polymerase I
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0045945 positive regulation of transcription by RNA polymerase III
GO:0140374 antiviral innate immune response
GO:1905213 negative regulation of mitotic chromosome condensation
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0000793 condensed chromosome
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005677 chromatin silencing complex
GO:0005694 chromosome
GO:0005721 pericentric heterochromatin
GO:0005730 nucleolus
GO:0008623 CHRAC
GO:0016589 NURF complex
GO:0016590 ACF complex
GO:0031010 ISWI-type complex
GO:0031213 RSF complex
GO:0035861 site of double-strand break
GO:0043596 nuclear replication fork
GO:0090535 WICH complex
GO:0090536 NoRC complex
GO:0110016 B-WICH complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8v6v, PDBe:8v6v, PDBj:8v6v
PDBsum8v6v
PubMed38472177
UniProtO60264|SMCA5_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (Gene Name=SMARCA5)

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