Structure of PDB 8bot Chain C

Receptor sequence
>8botC (length=511) Species: 9606 (Homo sapiens) [Search protein sequence]
NKAAVVLCMDTMSNESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDG
TDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIV
SMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQF
FLPFKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKI
ERHSIHWPCRLTIGLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKE
TVYCLNDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVL
GFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIV
RYAYDKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKK
YAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQC
LLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAK
KKDQVTAQEIF
3D structure
PDB8bot Cryo-EM structure of a DNA-PK trimer: higher order oligomerisation in NHEJ.
ChainC
Resolution7.76 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.6.4.-
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 dna C H243 I245 A263 N359 Y397 R400 H203 I205 A221 N316 Y354 R357
BS02 dna C I245 H246 V272 Y397 D398 R400 I205 H206 V230 Y354 D355 R357
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8bot, PDBe:8bot, PDBj:8bot
PDBsum8bot
PubMed37311458
UniProtP13010|XRCC5_HUMAN X-ray repair cross-complementing protein 5 (Gene Name=XRCC5)

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