› 5nfn

X-ray diffraction
2.98Å resolution

JMJD7 IN COMPLEX WITH MN AND 2OG IN THE H32 FORM

Released:
DOI: 10.2210/pdb5nfn/pdb
PDB entry 5nfn coloured by chain, front view.
PDB entry 5nfn coloured by chain, side view.
PDB entry 5nfn coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Chowdhury R, Markolovic S, Schofield CJ

Function and Biology Details

Reaction catalysed: 
A [protein]-L-lysine + 2-oxoglutarate + O(2) = a [protein]-(3S)-hydroxy-L-lysine + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143166 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 335 amino acids
Theoretical weight: 38.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0C870 (Residues: 1-316; Coverage: 100%)
Gene name: JMJD7
Sequence domains: Cupin-like domain
Structure domains: Jelly Rolls

Ligands and Environments

4 bound ligands:
Ligand MN 4 x MN
Ligand AKG 3 x AKG
Ligand NO3 7 x NO3
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: R32
Unit cell:
a: 207.22Å b: 207.22Å c: 211.788Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.24 0.249 0.251
Expression system: Escherichia coli BL21(DE3)

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