› 5k4w

X-ray diffraction
1.72Å resolution

Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NADH and L-threonine refined to 1.72 angstroms

Released:
DOI: 10.2210/pdb5k4w/pdb
PDB entry 5k4w coloured by chain, front view.
PDB entry 5k4w coloured by chain, side view.
PDB entry 5k4w coloured by chain, top view.
Source organism: Trypanosoma brucei
Primary publication:
Structure and function of L-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations.
Adjogatse E, Erskine P, Wells SA, Kelly JM, Wilden JD, Chan AWE, Selwood D, Coker A, Wood S, Cooper JB
Acta Crystallogr D Struct Biol 74 861-876 (2018)
PMID: 30198897

Function and Biology Details

Reaction catalysed: 
L-threonine + NAD(+) = L-2-amino-3-oxobutanoate + NADH
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182221 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-dependent epimerase/dehydratase domain-containing protein Chains: A, C
Molecule details ›
Chains: A, C
Length: 321 amino acids
Theoretical weight: 35.85 KDa
Source organism: Trypanosoma brucei
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7YW97 (Residues: 14-332; Coverage: 100%)
Sequence domains: NAD dependent epimerase/dehydratase family
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAI 2 x NAI
3 bound ligands:
Ligand THR 2 x THR
Ligand GOL 3 x GOL
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21212
Unit cell:
a: 83.45Å b: 136.12Å c: 55.69Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.152 0.198
Expression system: Escherichia coli

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Citations

1 review citation

Why is manganese so valuable to bacterial pathogens?
Čapek et al. (2023)
1 other article