Structure of PDB 5kgf Chain D Binding Site BS02

Receptor Information

>5kgf Chain D (length=100) Species: 9606 (Homo sapiens)

GKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAG
EASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Ligand information

>5kgf Chain J (length=145)

atcgatgtatatatctgacacgtgcctggagactagggagtaatcccctt
ggcggttaaaacgcgggggacagcgcgtacgtgcgtttaagcggtgctag
agctgtctacgaccaattgagcggcctcggcaccgggattctgat

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5kgf The structural basis of modified nucleosome recognition by 53BP1.
• Resolution: 4.54 Å
• Binding residue (original residue number in PDB): K24 K25 R26 R28 R30 K31 E32 Y37
• Binding residue (residue number reindexed from 1): K2 K3 R4 R6 R8 K9 E10 Y15

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0005515 protein binding
• GO:0030527 structural constituent of chromatin
• GO:0042802 identical protein binding
• GO:0046982 protein heterodimerization activity

Biological Process

• GO:0002227 innate immune response in mucosa
• GO:0006334 nucleosome assembly
• GO:0019731 antibacterial humoral response
• GO:0042742 defense response to bacterium
• GO:0050830 defense response to Gram-positive bacterium
• GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide

Cellular Component

• GO:0000786 nucleosome
• GO:0005615 extracellular space
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005694 chromosome
• GO:0005829 cytosol
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:5kgf, PDBe:5kgf, PDBj:5kgf
• PDBsum: 5kgf
• PubMed: 27462807
• UniProt: P62807|H2B1C_HUMAN Histone H2B type 1-C/E/F/G/I (Gene Name=H2BC4)