Structure of PDB 8byq Chain 1 Binding Site BS01

Receptor Information
>8byq Chain 1 (length=760) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLNVDGLLVYFPYDYIYPEQFSYMRELKRTLDAKGHGVLEMPSGTGKTV
SLLALIMAYQRAYPLEVTKLIYCSRTVPEIEKVIEELRKLLNFYEKQEGE
KLPFLGLALSSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDT
SLPHCRFYEEFDAHGREVPLPAGIYNLDDLKALGRRQGWCPYFLARYSIL
HANVVVYSYHYLLDPKIADLVSKELARKAVVVFDEAHNIDNVCIDSMSVN
LTRRTLDRCQGNLETLQKTVLRIKETDEQRLRDEYRRLVEGLREASAARE
TDAHLANPVLPDEVLQEAVPGSIRTAEHFLGFLRRLLEYVKWRLRVQHVV
QESPPAFLSGLAQRVCIQRKPLRFCAERLRSLLHTLEITDLADFSPLTLL
ANFATLVSTYAKGFTIIIEPFDDRTPTIANPILHFSCMDASLAIKPVFER
FQSVIITSGTLSPLDIYPKILDFHPVTMATFTMTLARVCLCPMIIGRGND
QVAISSKFETREDIAVIRNYGNLLLEMSAVVPDGIVAFFTSYQYMESTVA
SWYEQGILENIQRNKLLFIETQDGAETSVALEKYQEACENGRGAILLSVA
RGKVSEGIDFVHHYGRAVIMFGVPYVYTQSRILKARLEYLRDQFQIREND
FLTFDAMRHAAQCVGRAIRGKTDYGLMVFADKRFARGDKRGKLPRWIQEH
LTDANLNLTVDEGVQVAKYFLRQMAQPFHREDQLGLSLLSLEQLESEETL
KRIEQIAQQL
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 chain8byq Chain 1 Residue 1000 [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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PDB8byq Structural basis of transcription reduction by a promoter-proximal +1 nucleosome.
Resolution4.1 Å
Binding residue
(original residue number in PDB)		R112 C116 I117 H118 V121 C134 C155 F157 C190 F193
Binding residue
(residue number reindexed from 1)		R112 C116 I117 H118 V121 C134 C155 F157 C190 F193
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: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:0030674 protein-macromolecule adaptor activity
GO:0043139 5'-3' DNA helicase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0001666 response to hypoxia
GO:0001701 in utero embryonic development
GO:0006139 nucleobase-containing compound metabolic process
GO:0006259 DNA metabolic process
GO:0006281 DNA repair
GO:0006283 transcription-coupled nucleotide-excision repair
GO:0006289 nucleotide-excision repair
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006362 transcription elongation by RNA polymerase I
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0006915 apoptotic process
GO:0006974 DNA damage response
GO:0006979 response to oxidative stress
GO:0007059 chromosome segregation
GO:0008340 determination of adult lifespan
GO:0009411 response to UV
GO:0009650 UV protection
GO:0009791 post-embryonic development
GO:0021510 spinal cord development
GO:0022405 hair cycle process
GO:0030198 extracellular matrix organization
GO:0030282 bone mineralization
GO:0032289 central nervous system myelin formation
GO:0032508 DNA duplex unwinding
GO:0035264 multicellular organism growth
GO:0035315 hair cell differentiation
GO:0040016 embryonic cleavage
GO:0042274 ribosomal small subunit biogenesis
GO:0043249 erythrocyte maturation
GO:0043588 skin development
GO:0045951 positive regulation of mitotic recombination
GO:0048009 insulin-like growth factor receptor signaling pathway
GO:0048568 embryonic organ development
GO:0048820 hair follicle maturation
GO:0060218 hematopoietic stem cell differentiation
GO:0071425 hematopoietic stem cell proliferation
GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator
GO:1901990 regulation of mitotic cell cycle phase transition
Cellular Component
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:0005737 cytoplasm
GO:0005819 spindle
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0070516 CAK-ERCC2 complex
GO:0071817 MMXD complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8byq, PDBe:8byq, PDBj:8byq
PDBsum8byq
PubMed37148879
UniProtP18074|ERCC2_HUMAN General transcription and DNA repair factor IIH helicase subunit XPD (Gene Name=ERCC2)

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