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Crystal structure of JARID1A-PHD3 complexed with H3(1-9) K4ME3 peptide

Analyse Crystal structure of JARID1A-PHD3 complexed with H3(1-9) K4ME3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GL6
Type: protein
Length: 60 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone demethylase JARID1A; Histone H3
EC: 1.14.11.-
UniProt: P29375
Ligands: ZN

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone demethylase JARID1A (EC 1.14.11.-)	protein	52	17% helix, 17% strand	P29375
B	Histone H3	protein	8	0% helix, 63% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

A–B · 627 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (methylation).

Compared structures

3GL6 · Crystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
P29375 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5A (P29375) · a predicted model of the same protein · chain A against A, TM-score 0.73

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P29375
Elsewhere: RCSB PDB 3GL6 · PDBe 3GL6 · UniProt P29375

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