Structure of PDB 7ml1 Chain 0 Binding Site BS01

Receptor Information
>7ml1 Chain 0 (length=754) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKFYIDDLPVLFPYPKIYPEQYNYMCDIKKTLDVGGNSILEMPSGTGKTV
SLLSLTIAYQMHYPEHRKIIYCSRTMSEIEKALVELENLMDYRTKELGYQ
EDFRGLGLTSRKNLCLHPEVSKERKGTVVDEKCRRMTNGQAKRKLEEDPE
ANVELCEYHENLYNIEVEDYLPKGVFSFEKLLKYCEEKTLCPYFIVRRMI
SLCNIIIYSYHYLLDPKIAERVSNEVSKDSIVIFDEAHNIDNVCIESLSL
DLTTDALRRATRGANALDERISEVRKVDSQKLQDEYEKLVQGLHSADILT
DQEEPFVETPVLPQDLLTEAIPGNIRRAEHFVSFLKRLIEYLKTRMKVLH
VISETPKSFLQHLKQLTFIERKPLRFCSERLSLLVRTLEVTEVEDFTALK
DIATFATLISTYEEGFLLIIEPYEIENAAVPNPIMRFTCLDASIAIKPVF
ERFSSVIITSGTISPLDMYPRMLNFKTVLQKSYAMTLAKKSFLPMIITKG
SDQVAISSRFEIRNDPSIVRNYGSMLVEFAKITPDGMVVFFPSYLYMESI
VSMWQTMGILDEVWKHKLILVETPDAQETSLALETYRKACSNGRGAILLS
VARGKVSEGIDFDHQYGRTVLMIGIPFQYTESRILKARLEFMRENYRIRE
NDFLSFDAMRHAAQCLGRVLRGKDDYGVMVLADRRFSRKRSQLPKWIAQG
LSDADLNLSTDMAISNTKQFLRTMAQPTDPKDQEGVSVWSYEDLIKHQNS
RKDQ
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain7ml1 Chain 0 Residue 801 [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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PDB7ml1 Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Resolution4.0 Å
Binding residue
(original residue number in PDB)		C115 L116 H117 V120 C133 T137 C156 Y158 H159 C191 Y193 F194
Binding residue
(residue number reindexed from 1)		C115 L116 H117 V120 C133 T137 C156 Y158 H159 C191 Y193 F194
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
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:0008094 ATP-dependent activity, acting on DNA
GO:0016787 hydrolase activity
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0016853 isomerase activity
GO:0016887 ATP hydrolysis activity
GO:0043139 5'-3' DNA helicase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0000019 regulation of mitotic recombination
GO:0006139 nucleobase-containing compound metabolic process
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:0006974 DNA damage response
GO:0032508 DNA duplex unwinding
GO:0045951 positive regulation of mitotic recombination
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:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7ml1, PDBe:7ml1, PDBj:7ml1
PDBsum7ml1
PubMed35051353
UniProtP06839|RAD3_YEAST General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 (Gene Name=RAD3)

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