Structure of PDB 5oaf Chain D Binding Site BS01

Receptor Information
>5oaf Chain D (length=411) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIRE
GKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSK
TEALTQAFRRSIGVRIKEETEIIEGEVVEIQGKLTLKTTEMETIYDLGTK
MIESLTKDKVQAGDVITIDKATGKISKLGRSFTTKFVQCPDGELQKRKEV
VHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGK
AEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGT
SYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYT
VLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESR
STQYMKEYQDA
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 chain5oaf Chain D 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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PDB5oaf Cryo-EM structures of the human INO80 chromatin-remodeling complex.
Resolution4.06 Å
Binding residue
(original residue number in PDB)		H25 P79 G80 T81 G82 K83 T84 A85 Y362 R400 I403
Binding residue
(residue number reindexed from 1)		H10 P64 G65 T66 G67 K68 T69 A70 Y324 R362 I365
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding
GO:0001094 TFIID-class transcription factor complex binding
GO:0003678 DNA helicase activity
GO:0003714 transcription corepressor activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008013 beta-catenin binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0017025 TBP-class protein binding
GO:0031490 chromatin DNA binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0043531 ADP binding
GO:0051082 unfolded protein binding
GO:0051117 ATPase binding
GO:0140585 promoter-enhancer loop anchoring activity
Biological Process
GO:0000492 box C/D snoRNP assembly
GO:0000723 telomere maintenance
GO:0006275 regulation of DNA replication
GO:0006281 DNA repair
GO:0006282 regulation of DNA repair
GO:0006310 DNA recombination
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006355 regulation of DNA-templated transcription
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006457 protein folding
GO:0032508 DNA duplex unwinding
GO:0033044 regulation of chromosome organization
GO:0034644 cellular response to UV
GO:0042981 regulation of apoptotic process
GO:0045739 positive regulation of DNA repair
GO:0045892 negative regulation of DNA-templated transcription
GO:0045893 positive regulation of DNA-templated transcription
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0045995 regulation of embryonic development
GO:0050821 protein stabilization
GO:0051276 chromosome organization
GO:0051726 regulation of cell cycle
GO:0060382 regulation of DNA strand elongation
GO:0071169 establishment of protein localization to chromatin
GO:0071392 cellular response to estradiol stimulus
GO:0090090 negative regulation of canonical Wnt signaling pathway
GO:0090671 telomerase RNA localization to Cajal body
GO:1904507 positive regulation of telomere maintenance in response to DNA damage
GO:1905168 positive regulation of double-strand break repair via homologous recombination
GO:2000779 regulation of double-strand break repair
Cellular Component
GO:0000786 nucleosome
GO:0000791 euchromatin
GO:0000812 Swr1 complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005829 cytosol
GO:0016020 membrane
GO:0016363 nuclear matrix
GO:0031011 Ino80 complex
GO:0035267 NuA4 histone acetyltransferase complex
GO:0070062 extracellular exosome
GO:0071339 MLL1 complex
GO:0097255 R2TP complex
GO:0101031 protein folding chaperone complex
GO:0120293 dynein axonemal particle
GO:1990062 RPAP3/R2TP/prefoldin-like complex
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5oaf, PDBe:5oaf, PDBj:5oaf
PDBsum5oaf
PubMed29323271
UniProtQ9Y230|RUVB2_HUMAN RuvB-like 2 (Gene Name=RUVBL2)

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