› 5ly2

X-ray diffraction
2.43Å resolution

JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Macrocyclic PEPTIDE Inhibitor CP2_R6Kme3 (13-mer)

Released:
DOI: 10.2210/pdb5ly2/pdb
PDB entry 5ly2 coloured by chain, front view.
PDB entry 5ly2 coloured by chain, side view.
PDB entry 5ly2 coloured by chain, top view.
Source organisms:
Primary publication:
Highly selective inhibition of histone demethylases by de novo macrocyclic peptides.
Kawamura A, Münzel M, Kojima T, Yapp C, Bhushan B, Goto Y, Tumber A, Katoh T, King ON, Passioura T, Walport LJ, Hatch SB, Madden S, Müller S, Brennan PE, Chowdhury R, Hopkinson RJ, Suga H, Schofield CJ
OpenAccess logo Nat Commun 8 14773 (2017)
PMID: 28382930

Function and Biology Details

Reactions catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(9) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) + succinate + formaldehyde + CO(2)
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(36) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(36) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130877 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase 4A Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 381 amino acids
Theoretical weight: 44.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75164 (Residues: 1-359; Coverage: 34%)
Gene names: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677
Sequence domains:
Structure domains: Cupin
CP2_R6Kme3 Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 14 amino acids
Theoretical weight: 1.93 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand NI 4 x NI
Ligand ZN 4 x ZN
Ligand OGA 4 x OGA
Ligand GOL 5 x GOL
Ligand CL 5 x CL
2 modified residues:
Ligand DTY 4 x DTY
Ligand M3L 4 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21
Unit cell:
a: 58.306Å b: 103.747Å c: 142.367Å
α: 90° β: 99.14° γ: 90°
R-values:
R R work R free
0.22 0.219 0.245
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

18 review citations

2-Oxoglutarate-Dependent Oxygenases.
Islam et al. (2018)
17 more

1 mention without citation

Highly selective inhibition of histone demethylases by de novo macrocyclic peptides.
Kawamura et al. (2017)