Structure of PDB 8ezb Chain J Binding Site BS03

Receptor Information
>8ezb Chain J (length=497) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISSD
RDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQK
RFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGND
SAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISVHFEESS
KLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIK
LYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEEL
KRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLI
KCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFL
PFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHF
RNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDY
Ligand information
>8ezb Chain T (length=23) Species: 9606 (Homo sapiens) [Search peptide sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
RCPGESLINPGFKSKKPAGGVDF
Receptor-Ligand Complex Structure
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PDB8ezb Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ.
Resolution8.9 Å
Binding residue
(original residue number in PDB)		D36 K74 R165 K238 D241 L242 E250 R252 L469 R470 F471 S477 K510 R517
Binding residue
(residue number reindexed from 1)		D7 K45 R136 K201 D204 L205 E213 R215 L432 R433 F434 S440 K473 R480
Enzymatic activity
Enzyme Commision number 3.6.4.-
4.2.99.-
Gene Ontology
Molecular Function
GO:0000976 transcription cis-regulatory region binding
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0003684 damaged DNA binding
GO:0003690 double-stranded DNA binding
GO:0003691 double-stranded telomeric DNA binding
GO:0003723 RNA 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:0016829 lyase activity
GO:0016887 ATP hydrolysis activity
GO:0030332 cyclin binding
GO:0042162 telomeric DNA binding
GO:0044877 protein-containing complex binding
GO:0045027 DNA end binding
GO:0051575 5'-deoxyribose-5-phosphate lyase activity
GO:0097110 scaffold protein binding
Biological Process
GO:0000723 telomere maintenance
GO:0000725 recombinational repair
GO:0002218 activation of innate immune response
GO:0006266 DNA ligation
GO:0006281 DNA repair
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006310 DNA recombination
GO:0010558 negative regulation of macromolecule biosynthetic process
GO:0032508 DNA duplex unwinding
GO:0045087 innate immune response
GO:0045621 positive regulation of lymphocyte differentiation
GO:0045860 positive regulation of protein kinase activity
GO:0045892 negative regulation of DNA-templated transcription
GO:0045893 positive regulation of DNA-templated transcription
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0048660 regulation of smooth muscle cell proliferation
GO:0071475 cellular hyperosmotic salinity response
GO:0071480 cellular response to gamma radiation
GO:0071481 cellular response to X-ray
GO:0097680 double-strand break repair via classical nonhomologous end joining
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0000783 nuclear telomere cap complex
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription regulator complex
GO:0005694 chromosome
GO:0005730 nucleolus
GO:0005829 cytosol
GO:0005958 DNA-dependent protein kinase-DNA ligase 4 complex
GO:0016020 membrane
GO:0032991 protein-containing complex
GO:0032993 protein-DNA complex
GO:0034774 secretory granule lumen
GO:0043564 Ku70:Ku80 complex
GO:0070418 DNA-dependent protein kinase complex
GO:0070419 nonhomologous end joining complex
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8ezb, PDBe:8ezb, PDBj:8ezb
PDBsum8ezb
PubMed37256947
UniProtP12956|XRCC6_HUMAN X-ray repair cross-complementing protein 6 (Gene Name=XRCC6)

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