Structure of PDB 5cpj Chain D

Receptor sequence

>5cpjD (length=93) Species: 9606 (Homo sapiens) [Search protein sequence]

SRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLA
HYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

3D structure

PDB

5cpj Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.

Chain

Resolution

3.15 Å

3D
structure

Enzymatic activity

Enzyme Commision number

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	D	R33 K34 Y42 G53 I54 S55 S56 R86 S87	R2 K3 Y11 G22 I23 S24 S25 R55 S56
BS02	dna	D	R33 Y40	R2 Y9

Gene Ontology

	Molecular Function
GO:0001530	lipopolysaccharide binding
GO:0003677	DNA binding
GO:0005515	protein binding
GO:0030527	structural constituent of chromatin
GO:0046982	protein heterodimerization activity

	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

External links

PDB	RCSB:5cpj, PDBe:5cpj, PDBj:5cpj
PDBsum	5cpj
PubMed	26446621
UniProt	P06899\|H2B1J_HUMAN Histone H2B type 1-J (Gene Name=H2BC11)