› 3puq

X-ray diffraction
2.25Å resolution

CEKDM7A from C.Elegans, complex with alpha-KG

Released:
DOI: 10.2210/pdb3puq/pdb
Model geometry
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PDB entry 3puq coloured by chain, front view.
PDB entry 3puq coloured by chain, side view.
PDB entry 3puq coloured by chain, top view.
Source organism: Caenorhabditis elegans
Primary publication:
Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases.
Xu W, Yang H, Liu Y, Yang Y, Wang P, Kim SH, Ito S, Yang C, Wang P, Xiao MT, Liu LX, Jiang WQ, Liu J, Zhang JY, Wang B, Frye S, Zhang Y, Xu YH, Lei QY, Guan KL, Zhao SM, Xiong Y
Cancer Cell 19 17-30 (2011)
PMID: 21251613

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190436 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 7 homolog Chains: A, C
Molecule details ›
Chains: A, C
Length: 528 amino acids
Theoretical weight: 61.95 KDa
Source organism: Caenorhabditis elegans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9GYI0 (Residues: 201-724; Coverage: 58%)
Gene names: F29B9.2, jmjd-1.2
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand FE2 2 x FE2
Ligand ZN 4 x ZN
Ligand AKG 2 x AKG
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 93.592Å b: 78.138Å c: 102.93Å
α: 90° β: 92.07° γ: 90°
R-values:
R R work R free
0.189 0.188 0.224
Expression system: Escherichia coli

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Citations

789 review citations

The Emerging Hallmarks of Cancer Metabolism.
Pavlova et al. (2016)
788 more

3 mentions without citation

Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives.
Andreoli et al. (2013)
2 more

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