Structure of PDB 7nvx Chain 7 Binding Site BS06

Receptor Information

>7nvx Chain 7 (length=605) Species: 9606 (Homo sapiens)

TKVDEYGAKDYRLQMPLKDDHTSRPLWVAPDGHIFLEAFSPVYKYAQDFL
VAIAEPVCRPTHVHEYKLTAYSLYAAVSVGLQTSDITEYLRKLSKTGVPD
GIMQFIKLCTVSYGKVKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLR
QTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVNPDINIDLKPTAV
LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG
NSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGH
TTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLG
LTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMS
PEFYREYVAIKTKKRILLYTMNPNKFRACQFLIKFHERRNDKIIVFADNV
FALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSF
DLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQ
DTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTKEEQQQLLQK
VLAAT

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:
  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
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 7nvx Chain 7 Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7nvx Structures of mammalian RNA polymerase II pre-initiation complexes.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): R317 G343 G345 K346 S347 D616 R645
• Binding residue (residue number reindexed from 1): R202 G228 G230 K231 S232 D501 R530
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 5.6.2.4: DNA 3'-5' helicase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003678 DNA helicase activity
• GO:0003684 damaged DNA binding
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity
• GO:0016853 isomerase activity
• GO:0016887 ATP hydrolysis activity
• GO:0043138 3'-5' DNA helicase activity
• GO:1990841 promoter-specific chromatin binding

Biological Process

• GO:0000717 nucleotide-excision repair, DNA duplex unwinding
• GO:0001666 response to hypoxia
• GO:0006265 DNA topological change
• GO:0006281 DNA repair
• GO:0006283 transcription-coupled nucleotide-excision repair
• GO:0006289 nucleotide-excision repair
• GO:0006366 transcription by RNA polymerase II
• GO:0006367 transcription initiation at RNA polymerase II promoter
• GO:0006368 transcription elongation by RNA polymerase II
• GO:0006915 apoptotic process
• GO:0006979 response to oxidative stress
• GO:0008104 protein localization
• GO:0009411 response to UV
• GO:0009650 UV protection
• GO:0035315 hair cell differentiation
• GO:0043065 positive regulation of apoptotic process
• GO:0048568 embryonic organ development
• GO:1901990 regulation of mitotic cell cycle phase transition

Cellular Component

• GO:0000112 nucleotide-excision repair factor 3 complex
• GO:0000439 transcription factor TFIIH core complex
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005669 transcription factor TFIID complex
• GO:0005675 transcription factor TFIIH holo complex
• GO:0097550 transcription preinitiation complex

External links

• PDB: RCSB:7nvx, PDBe:7nvx, PDBj:7nvx
• PDBsum: 7nvx
• PubMed: 33902107
• UniProt: P19447|ERCC3_HUMAN General transcription and DNA repair factor IIH helicase/translocase subunit XPB (Gene Name=ERCC3)