› 3kbo

X-ray diffraction
2.14Å resolution

2.14 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium in Complex with NADP

Released:
DOI: 10.2210/pdb3kbo/pdb
PDB entry 3kbo coloured by chain, front view.
PDB entry 3kbo coloured by chain, side view.
PDB entry 3kbo coloured by chain, top view.
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Entry authors: Minasov G, Wawrzak Z, Skarina T, Onopriyenko O, Papazisi L, Savchenko A, Anderson WF, Center for Structural Genomics of Infectious Diseases (CSGID)

Function and Biology Details

Reactions catalysed: 
Glycolate + NADP(+) = glyoxylate + NADPH
D-glycerate + NAD(P)(+) = hydroxypyruvate + NAD(P)H
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187356 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glyoxylate/hydroxypyruvate reductase A Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 315 amino acids
Theoretical weight: 35.72 KDa
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8ZQ30 (Residues: 1-312; Coverage: 100%)
Gene names: STM1135, ghrA
Sequence domains: D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NDP 4 x NDP
3 bound ligands:
Ligand NDB 1 x NDB
Ligand CL 8 x CL
Ligand EPE 2 x EPE
1 modified residue:
Ligand MSE 32 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2
Unit cell:
a: 279.621Å b: 45.585Å c: 112.335Å
α: 90° β: 101.58° γ: 90°
R-values:
R R work R free
0.214 0.211 0.269
Expression system: Escherichia coli

Quick links