Structure of PDB 7o4j Chain 7 Binding Site BS04

Receptor Information
>7o4j Chain 7 (length=615) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PADFVPDSVSGMFRSHDFSYLRLRPDHASRPLWISPSDGRIILESFSPLA
EQAQDFLVTIAEPISRPSHIHEYKITAYSLYAAVSVGLETDDIISVLDRL
SKVPVAESIINFIKGATISYGKVKLVIKHNRYFVETTQADILQMLLNDSV
IGVHSFEIANESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLDIDLKPST
QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVL
CTSSVSVMQWRQQFLQWCTLQPENCAVFTSDNKEMFQTESGLVVSTYSMV
ANTRNRSHDSQKVMDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAK
LGLTATLVREDDKIGDLNFLIGPKLYEANWMELSQKGHIANVQCAEVWCP
MTAEFYQEYLRETARKRMLLYIMNPTKFQACQFLIQYHERRGDKIIVFSD
NVYALQEYALKMGKPFIYGSTPQQERMNILQNFQYNDQINTIFLSKVGDT
SIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVS
KDTQEMYYSTKRQAFLVDQGYAFKVITHLHGMENIPNLAYASPRERRELL
QEVLLKNHPLIRKMY
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 chain7o4j Chain 7 Residue 903 [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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PDB7o4j Structure of RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		R363 G389 G391 K392 T393 W427 D663 R692
Binding residue
(residue number reindexed from 1)		R203 G229 G231 K232 T233 W267 D503 R532
Annotation score5
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:0004386 helicase activity
GO:0005524 ATP binding
GO:0015616 DNA translocase activity
GO:0016787 hydrolase activity
GO:0016853 isomerase activity
GO:0016887 ATP hydrolysis activity
GO:0043138 3'-5' DNA helicase activity
Biological Process
GO:0000019 regulation of mitotic recombination
GO:0001111 RNA polymerase II promoter clearance
GO:0001113 transcription open complex formation at RNA polymerase II promoter
GO:0001174 transcriptional start site selection at RNA polymerase II promoter
GO:0006281 DNA repair
GO:0006289 nucleotide-excision repair
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0016973 poly(A)+ mRNA export from nucleus
GO:0032508 DNA duplex unwinding
Cellular Component
GO:0000112 nucleotide-excision repair factor 3 complex
GO:0000439 transcription factor TFIIH core complex
GO:0005634 nucleus
GO:0005675 transcription factor TFIIH holo complex
GO:0005829 cytosol
GO:0097550 transcription preinitiation complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7o4j, PDBe:7o4j, PDBj:7o4j
PDBsum7o4j
PubMed34133942
UniProtQ00578|RAD25_YEAST General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 (Gene Name=SSL2)

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