› 8jdv

X-ray diffraction
1.96Å resolution

Crystal structure of mLDHD in complex with 2-ketohexanoic acid

Released:
DOI: 10.2210/pdb8jdv/pdb
PDB entry 8jdv coloured by chain, front view.
PDB entry 8jdv coloured by chain, side view.
PDB entry 8jdv coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Lactate dehydrogenase D is a general dehydrogenase for D-2-hydroxyacids and is associated with D-lactic acidosis.
Jin S, Chen X, Yang J, Ding J
OpenAccess logo Nat Commun 14 6638 (2023)
PMID: 37863926

Function and Biology Details

Reaction catalysed: 
(R)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c + 2 H(+)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-232496 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable D-lactate dehydrogenase, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 471 amino acids
Theoretical weight: 50.45 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7TNG8 (Residues: 22-484; Coverage: 96%)
Gene name: Ldhd
Sequence domains:

Ligands and Environments


Cofactor: Ligand FAD 1 x FAD
2 bound ligands:
Ligand MN 1 x MN
Ligand 7N5 1 x 7N5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: I222
Unit cell:
a: 82.782Å b: 101.403Å c: 124.58Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.205
Expression system: Escherichia coli

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