› 6dq7

X-ray diffraction
1.85Å resolution

LINKED KDM5A JMJ DOMAIN BOUND TO THE POTENTIAL HYDROLYSIS PRODUCT OF INHIBITOR N45 i.e. 3-((6-(4-(2-cyano-3-methylbut-2-enoyl)-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid

Released:
DOI: 10.2210/pdb6dq7/pdb
PDB entry 6dq7 coloured by chain, front view.
PDB entry 6dq7 coloured by chain, side view.
PDB entry 6dq7 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Horton JR, Cheng X

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(4) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151436 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 5A Chain: A
Molecule details ›
Chain: A
Length: 330 amino acids
Theoretical weight: 37.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P29375 (Residues: 1-588; Coverage: 19%)
Gene names: JARID1A, KDM5A, RBBP2, RBP2
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand H6M 1 x H6M
Ligand MN 1 x MN
Ligand EDO 1 x EDO
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: C2
Unit cell:
a: 117.506Å b: 62.309Å c: 46.695Å
α: 90° β: 92.39° γ: 90°
R-values:
R R work R free
0.193 0.192 0.209
Expression system: Escherichia coli BL21(DE3)

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