› 3deq

X-ray diffraction
2.1Å resolution

Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Leu dipeptide

Released:
DOI: 10.2210/pdb3deq/pdb
Model geometry
Fit model/data
PDB entry 3deq coloured by chain, front view.
PDB entry 3deq coloured by chain, side view.
PDB entry 3deq coloured by chain, top view.
Source organism: Thermotoga maritima MSB8
Primary publication:
Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.
Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP
Structure 16 1668-77 (2008)
PMID: 19000819

Function and Biology Details

Reaction catalysed: 
L-alanyl-D-glutamate = L-alanyl-L-glutamate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo octamer
Assembly name:
PDBe Complex ID:
PDB-CPX-194422 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-Ala-D/L-Glu epimerase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 345 amino acids
Theoretical weight: 38.72 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9WXM1 (Residues: 1-345; Coverage: 100%)
Gene name: TM_0006
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MG 4 x MG
Ligand ALA 4 x ALA
Ligand LEU 4 x LEU
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P6122
Unit cell:
a: 191.581Å b: 191.581Å c: 283.234Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.246 0.246 0.259
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Docking Screens for Novel Ligands Conferring New Biology.
Irwin et al. (2016)
7 more

2 mentions without citation

Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.
Kalyanaraman et al. (2008)
1 more