6f4t

X-ray diffraction
1.22Å resolution

Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)

Released:
Source organism: Homo sapiens

Function and Biology Details

Reaction catalysed:
[Protein]-L-arginine + 2-oxoglutarate + O(2) = [protein]-(3R)-3-hydroxy-L-arginine + succinate + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
PDBe Complex ID:
PDB-CPX-185372 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Bifunctional peptidase and arginyl-hydroxylase JMJD5 Chain: A
Molecule details ›
Chain: A
Length: 255 amino acids
Theoretical weight: 29.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8N371 (Residues: 183-416; Coverage: 56%)
Gene names: JMJD5, KDM8
Sequence domains: Cupin-like domain
Structure domains: Cupin
RCC1 domain-containing protein 1 Chain: B
Molecule details ›
Chain: B
Length: 5 amino acids
Theoretical weight: 584 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: A6NED2 (Residues: 139-143; Coverage: 1%)
Gene name: RCCD1

Ligands and Environments

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 49.137Å b: 65.169Å c: 78.446Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.142 0.141 0.154
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided