Structure of PDB 8txx Chain K Binding Site BS01

Receptor Information
>8txx Chain K (length=30) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DRLLALQLQKEVDKEQNRQKGSPDEYHLRA
Ligand information
>8txx Chain I (length=147) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
atcgagaatcccggtgccgaggccgctcaattggtcgtagacagctctag
caccgcttaaacgcacgtacgcgctgtcccccgcgttttaaccgccaagg
ggattactccctagtctccaggcacgtgtcagatatatacatccgat
Receptor-Ligand Complex Structure
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PDB8txx Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3)
Resolution3.7 Å
Binding residue
(original residue number in PDB)		L448 Q452
Binding residue
(residue number reindexed from 1)		L3 Q7
Enzymatic activity
Enzyme Commision number 2.3.2.27: RING-type E3 ubiquitin transferase.
Gene Ontology
Molecular Function
GO:0003682 chromatin binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0031491 nucleosome binding
GO:0042393 histone binding
GO:0043130 ubiquitin binding
GO:0046872 metal ion binding
GO:0070530 K63-linked polyubiquitin modification-dependent protein binding
GO:0140852 histone ubiquitin ligase activity
GO:0140858 histone H2AK15 ubiquitin ligase activity
Biological Process
GO:0006281 DNA repair
GO:0006302 double-strand break repair
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006325 chromatin organization
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006974 DNA damage response
GO:0010212 response to ionizing radiation
GO:0016567 protein ubiquitination
GO:0034244 negative regulation of transcription elongation by RNA polymerase II
GO:0036297 interstrand cross-link repair
GO:0040029 epigenetic regulation of gene expression
GO:0045190 isotype switching
GO:0045739 positive regulation of DNA repair
GO:0070534 protein K63-linked ubiquitination
GO:0097680 double-strand break repair via classical nonhomologous end joining
GO:0140861 DNA repair-dependent chromatin remodeling
Cellular Component
GO:0000151 ubiquitin ligase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex
GO:0035861 site of double-strand break

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8txx, PDBe:8txx, PDBj:8txx
PDBsum8txx
PubMed38242129
UniProtQ8IYW5|RN168_HUMAN E3 ubiquitin-protein ligase RNF168 (Gene Name=RNF168)

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