› 3ldb

X-ray diffraction
2.7Å resolution

Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.

Released:
DOI: 10.2210/pdb3ldb/pdb
PDB entry 3ldb coloured by chain, front view.
PDB entry 3ldb coloured by chain, side view.
PDB entry 3ldb coloured by chain, top view.
Source organisms:
Primary publication:
Interaction of JMJD6 with single-stranded RNA.
Hong X, Zang J, White J, Wang C, Pan CH, Zhao R, Murphy RC, Dai S, Henson P, Kappler JW, Hagman J, Zhang G
Proc Natl Acad Sci U S A 107 14568-72 (2010)
PMID: 20679243

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212390 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 Chain: A
Molecule details ›
Chain: A
Length: 334 amino acids
Theoretical weight: 39.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6NYC1 (Residues: 1-334; Coverage: 83%)
Gene names: JMJD6, KIAA0585, PSR, PTDSR
Sequence domains: JmjC domain, hydroxylase
Structure domains:
antibody Fab fragment light chain Chain: B
Molecule details ›
Chain: B
Length: 220 amino acids
Theoretical weight: 24.1 KDa
Source organism: Nothocricetulus migratorius
Expression system: Nothocricetulus migratorius
Structure domains: Immunoglobulins
antibody Fab fragment heavy chain Chain: C
Molecule details ›
Chain: C
Length: 221 amino acids
Theoretical weight: 24.01 KDa
Source organism: Nothocricetulus migratorius
Expression system: Nothocricetulus migratorius
Structure domains: Immunoglobulins

Ligands and Environments

5 bound ligands:
Ligand GOL 5 x GOL
Ligand SO4 19 x SO4
Ligand AKG 1 x AKG
Ligand FE 1 x FE
Ligand HG 2 x HG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1, ALS BEAMLINE 8.2.2
Spacegroup: P41212
Unit cell:
a: 138.381Å b: 138.381Å c: 183.622Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.25 0.25 0.285
Expression systems:
  • Escherichia coli
  • Nothocricetulus migratorius

Quick links

Citations

26 review citations

Protein arginine methyltransferases and cancer.
Yang et al. (2013)
25 more

8 mentions without citation

Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses.
Gao et al. (2018)
7 more