› 5nfo

X-ray diffraction
2.17Å resolution

Human JMJD7 in complex with Mn and 2OG in the P21212 form

Released:
DOI: 10.2210/pdb5nfo/pdb
PDB entry 5nfo coloured by chain, front view.
PDB entry 5nfo coloured by chain, side view.
PDB entry 5nfo 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
Molecule details ›
Chains: A, B
Length: 335 amino acids
Theoretical weight: 37.95 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 2 x MN
Ligand AKG 2 x AKG
Ligand GOL 6 x GOL
Ligand NO3 2 x NO3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21212
Unit cell:
a: 137.315Å b: 61.02Å c: 86.055Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.171 0.189
Expression system: Escherichia coli BL21(DE3)

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