Structure of PDB 7nkx Chain W Binding Site BS03

Receptor Information
>7nkx Chain W (length=622) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DFHGIDIVINHRLKTSKTVPDLNNCKENYEFLIKWTDESHLHNTWETYES
IGQVRGLKRLDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFE
EFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAP
EQVKHFQNRENSKILPQYSSNYTSQRPRFEKLSVQPPFIKGGELRDFQLT
GINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVV
PLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPKTMKFNV
LLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANR
MLITGTPLQNNIKELAALVNFLMPGRFNQDEEQEEYIHDLHRRIQPFILR
RLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSIMNELKKASNH
PYLFDNAEERVLTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQ
MVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLL
STRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRL
VSKDTVEEEVLERARKKMILEY
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 chain7nkx Chain W Residue 1501 [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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PDB7nkx Structural basis of nucleosome transcription mediated by Chd1 and FACT.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		E375 G404 L405 G406 K407 T408 W447 R807 I808
Binding residue
(residue number reindexed from 1)		E193 G222 L223 G224 K225 T226 W265 R588 I589
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.-
Gene Ontology
Molecular Function
GO:0000182 rDNA binding
GO:0000976 transcription cis-regulatory region binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0031490 chromatin DNA binding
GO:0035064 methylated histone binding
GO:0042393 histone binding
GO:0097159 organic cyclic compound binding
GO:0140658 ATP-dependent chromatin remodeler activity
Biological Process
GO:0000724 double-strand break repair via homologous recombination
GO:0000729 DNA double-strand break processing
GO:0001178 regulation of transcriptional start site selection at RNA polymerase II promoter
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006363 termination of RNA polymerase I transcription
GO:0006368 transcription elongation by RNA polymerase II
GO:0006369 termination of RNA polymerase II transcription
GO:0007062 sister chromatid cohesion
GO:0009889 regulation of biosynthetic process
GO:0034728 nucleosome organization
GO:1902275 regulation of chromatin organization
GO:2000104 negative regulation of DNA-templated DNA replication
Cellular Component
GO:0000123 histone acetyltransferase complex
GO:0000124 SAGA complex
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0030874 nucleolar chromatin
GO:0035861 site of double-strand break
GO:0046695 SLIK (SAGA-like) complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7nkx, PDBe:7nkx, PDBj:7nkx
PDBsum7nkx
PubMed33846633
UniProtP32657|CHD1_YEAST Chromo domain-containing protein 1 (Gene Name=CHD1)

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