Structure of PDB 4ym5 Chain D

Receptor sequence

>4ym5D (length=93) Species: 9606 (Homo sapiens) [Search protein sequence]

SRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLA
HYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

3D structure

PDB

4ym5 Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome

Chain

Resolution

4.005 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	S32 Y42 I54 S55 S56 R86 S87 T88	S1 Y11 I23 S24 S25 R55 S56 T57
BS02	dna	D	R33 K34 S36 I39 Y40	R2 K3 S5 I8 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:4ym5, PDBe:4ym5, PDBj:4ym5
PDBsum	4ym5
PubMed	26573481
UniProt	P06899\|H2B1J_HUMAN Histone H2B type 1-J (Gene Name=H2BC11)