Structure of PDB 5nbm Chain B Binding Site BS01

Receptor Information
>5nbm Chain B (length=397) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSEQSIGI
PRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPV
WNSTENRKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDT
CSVSPIVDGMTLSKSTRRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKP
EFIKKTFDYEVDKSLYDYANNRGFFQECKETLCHICPTKTLEETKTELSS
TAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDDIPANWPRSNSGVVEL
IGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPGLSDRLMTELNKIL
PSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVG
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 chain5nbm Chain B Residue 502 [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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PDB5nbm The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		G22 S23 Y24 T25 H162 Q240 K243 G413
Binding residue
(residue number reindexed from 1)		G8 S9 Y10 T11 H148 Q226 K229 G331
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0042393 histone binding
Biological Process
GO:0006281 DNA repair
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006351 DNA-templated transcription
GO:0006355 regulation of DNA-templated transcription
GO:0006357 regulation of transcription by RNA polymerase II
GO:0051382 kinetochore assembly
Cellular Component
GO:0000785 chromatin
GO:0000812 Swr1 complex
GO:0005634 nucleus
GO:0016514 SWI/SNF complex
GO:0031011 Ino80 complex
GO:0035267 NuA4 histone acetyltransferase complex
GO:0043232 intracellular non-membrane-bounded organelle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5nbm, PDBe:5nbm, PDBj:5nbm
PDBsum5nbm
PubMed30177756
UniProtP80428|ARP4_YEAST Actin-related protein 4 (Gene Name=ARP4)

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