Structure of PDB 8bot Chain C Binding Site BS02

Receptor Information

>8bot Chain C (length=511) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

NKAAVVLCMDTMSNESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDG
TDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIV
SMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQF
FLPFKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKI
ERHSIHWPCRLTIGLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKE
TVYCLNDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVL
GFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIV
RYAYDKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKK
YAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQC
LLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAK
KKDQVTAQEIF

Ligand information

>8bot Chain E (length=24) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

taataatagtttttagtttattag

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8bot Cryo-EM structure of a DNA-PK trimer: higher order oligomerisation in NHEJ.
Resolution	7.76 Å
Binding residue (original residue number in PDB)	I245 H246 V272 Y397 D398 R400
Binding residue (residue number reindexed from 1)	I205 H206 V230 Y354 D355 R357

Enzymatic activity

Enzyme Commision number

3.6.4.-

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:0008047	enzyme activator activity
GO:0008094	ATP-dependent activity, acting on DNA
GO:0016787	hydrolase activity
GO:0016887	ATP hydrolysis activity
GO:0031625	ubiquitin protein ligase binding
GO:0034511	U3 snoRNA 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

	Biological Process
GO:0000723	telomere maintenance
GO:0000725	recombinational repair
GO:0002218	activation of innate immune response
GO:0006281	DNA repair
GO:0006302	double-strand break repair
GO:0006303	double-strand break repair via nonhomologous end joining
GO:0006310	DNA recombination
GO:0006974	DNA damage response
GO:0007004	telomere maintenance via telomerase
GO:0009410	response to xenobiotic stimulus
GO:0010558	negative regulation of macromolecule biosynthetic process
GO:0022008	neurogenesis
GO:0032204	regulation of telomere maintenance
GO:0032508	DNA duplex unwinding
GO:0034462	small-subunit processome assembly
GO:0042254	ribosome biogenesis
GO:0045087	innate immune response
GO:0045860	positive regulation of protein kinase activity
GO:0045892	negative regulation of DNA-templated transcription
GO:0048660	regulation of smooth muscle cell proliferation
GO:0050769	positive regulation of neurogenesis
GO:0060218	hematopoietic stem cell differentiation
GO:0070198	protein localization to chromosome, telomeric region
GO:0071398	cellular response to fatty acid
GO:0071425	hematopoietic stem cell proliferation
GO:0071475	cellular hyperosmotic salinity response
GO:0071480	cellular response to gamma radiation
GO:0071481	cellular response to X-ray
GO:1904430	negative regulation of t-circle formation
GO:1990830	cellular response to leukemia inhibitory factor

	Cellular Component
GO:0000781	chromosome, telomeric region
GO:0000783	nuclear telomere cap complex
GO:0005576	extracellular region
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005694	chromosome
GO:0005730	nucleolus
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005886	plasma membrane
GO:0005958	DNA-dependent protein kinase-DNA ligase 4 complex
GO:0016020	membrane
GO:0032040	small-subunit processome
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:0090734	site of DNA damage
GO:1990904	ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:8bot, PDBe:8bot, PDBj:8bot
PDBsum	8bot
PubMed	37311458
UniProt	P13010\|XRCC5_HUMAN X-ray repair cross-complementing protein 5 (Gene Name=XRCC5)

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