Structure of PDB 5oaf Chain B Binding Site BS02

Receptor Information

>5oaf Chain B (length=418) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

VTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIRE
GKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSK
TEALTQAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGKLTLKT
TEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSFTRPDGE
LQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVA
EWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRG
ITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVE
MSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYS
LFLDESRSTQYMKEYQDA

Ligand information

Ligand ID

ADP

InChI

InChI=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

InChIKey

XTWYTFMLZFPYCI-KQYNXXCUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(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 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N

Formula

C10 H15 N5 O10 P2

Name

ADENOSINE-5'-DIPHOSPHATE

PDB chain

5oaf Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5oaf Cryo-EM structures of the human INO80 chromatin-remodeling complex.
Resolution	4.06 Å
Binding residue (original residue number in PDB)	A24 H27 M46 V47 Q78 P79 G80 T81 G82 K83 T84 A85 N329 Y362 I370 R400
Binding residue (residue number reindexed from 1)	A9 H12 M31 V32 Q63 P64 G65 T66 G67 K68 T69 A70 N298 Y331 I339 R369
Annotation score	5

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
PDBsum	5oaf
PubMed	29323271
UniProt	Q9Y230\|RUVB2_HUMAN RuvB-like 2 (Gene Name=RUVBL2)

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