Structure of PDB 8bhy Chain C

Receptor sequence

>8bhyC (length=668) Species: 9606 (Homo sapiens)

NKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIA
LVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQA
DFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLK
KCDISLQFFLPFSLGGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISL
EGEDGLDEIYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYK
SILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDDDETEVLKEDIIQGFR
YGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVF
AARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHN
YECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAK
KDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNM
LNPPAEVTTKSQIPLSKIKTLFPLIEAKKNPAENFRVLVKQKKASFEEAS
NQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLKALQ
EKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAKDKPSGD
TAAVFEEGGDVDDLLDMI

3D structure

• PDB: 8bhy PAXX binding to the NHEJ machinery explains functional redundancy with XLF.
• Chain: C
• Resolution: 5.33 Å

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	R271 K399 R400	R256 K384 R385
BS02	dna	C	R242 I245 K265 Y397 A401	R227 I230 K250 Y382 A386
BS03	peptide	C	V37 I38 F41 H131 E133 S160 L161 Q162 F164 L215 E216 D219 D222 E223 Y225 S230 K233 C235 V236 F237 K238 K239 I240	V32 I33 F36 H126 E128 S155 L156 Q157 F159 L200 E201 D204 D207 E208 Y210 S215 K218 C220 V221 F222 K223 K224 I225

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

External links

• PDB: RCSB:8bhy, PDBe:8bhy, PDBj:8bhy
• PDBsum: 8bhy
• PubMed: 37256950
• UniProt: P13010|XRCC5_HUMAN X-ray repair cross-complementing protein 5 (Gene Name=XRCC5)