Structure of PDB 8ybj Chain D Binding Site BS01

Receptor Information
>8ybj Chain D (length=92) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAH
YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA
Ligand information
>8ybj Chain I (length=145) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
atcagaatcccggtgccgaggccgctcaattggtcgtagacagctctagc
accgcttaaacgcacgtacgcgctgtcccccgcgttttaaccgccaaggg
gattactccctagtctccaggcacgtgtcagatatatacatcgat
Receptor-Ligand Complex Structure
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PDB8ybj Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K.
Resolution2.38 Å
Binding residue
(original residue number in PDB)		Y42 I54 S56 R86 S87 T88
Binding residue
(residue number reindexed from 1)		Y10 I22 S24 R54 S55 T56
Gene Ontology
Molecular Function
GO:0001530 lipopolysaccharide binding
GO:0003677 DNA binding
GO:0005515 protein binding
Biological Process
GO:0002227 innate immune response in mucosa
GO:0006325 chromatin organization
GO:0006334 nucleosome assembly
GO:0010804 negative regulation of tumor necrosis factor-mediated signaling pathway
GO:0019731 antibacterial humoral response
GO:0031640 killing of cells of another organism
GO:0042742 defense response to bacterium
GO:0050829 defense response to Gram-negative bacterium
GO:0050830 defense response to Gram-positive bacterium
GO:0061644 protein localization to CENP-A containing chromatin
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:0005886 plasma membrane
GO:0043505 CENP-A containing nucleosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8ybj, PDBe:8ybj, PDBj:8ybj
PDBsum8ybj
PubMed38972377
UniProtP06899|H2B1J_HUMAN Histone H2B type 1-J (Gene Name=H2BC11)

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