› 6lpt

X-ray diffraction
2.62Å resolution

Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-lactate (D-LAC)

Released:
DOI: 10.2210/pdb6lpt/pdb
Model geometry
Fit model/data
PDB entry 6lpt coloured by chain, front view.
PDB entry 6lpt coloured by chain, side view.
PDB entry 6lpt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations.
Yang J, Zhu H, Zhang T, Ding J
OpenAccess logo Cell Discov 7 3 (2021)
PMID: 33431826

Function and Biology Details

Reaction catalysed: 
(R)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185383 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-2-hydroxyglutarate dehydrogenase, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 481 amino acids
Theoretical weight: 52.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8N465 (Residues: 51-521; Coverage: 90%)
Gene names: D2HGD, D2HGDH
Sequence domains:

Ligands and Environments


Cofactor: Ligand FAD 2 x FAD
2 bound ligands:
Ligand ZN 2 x ZN
Ligand LAC 2 x LAC
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P21
Unit cell:
a: 72.263Å b: 94.411Å c: 73.575Å
α: 90° β: 111.77° γ: 90°
R-values:
R R work R free
0.193 0.191 0.231
Expression system: Escherichia coli

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Citations

7 citation in other articles

A D-2-hydroxyglutarate biosensor based on specific transcriptional regulator DhdR.
Xiao et al. (2021)
6 more

1 mention without citation

Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations.
Yang et al. (2021)