› 3k5x

X-ray diffraction
1.4Å resolution

Crystal structure of dipeptidase from Streptomics coelicolor complexed with phosphinate pseudodipeptide L-Ala-D-Asp at 1.4A resolution.

Released:
DOI: 10.2210/pdb3k5x/pdb
PDB entry 3k5x coloured by chain, front view.
PDB entry 3k5x coloured by chain, side view.
PDB entry 3k5x coloured by chain, top view.
Source organism: Streptomyces coelicolor
Primary publication:
Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase .
Cummings JA, Nguyen TT, Fedorov AA, Kolb P, Xu C, Fedorov EV, Shoichet BK, Barondeau DP, Almo SC, Raushel FM
Biochemistry 49 611-22 (2010)
PMID: 20000809

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-188078 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dipeptidase Chain: A
Molecule details ›
Chain: A
Length: 400 amino acids
Theoretical weight: 43.31 KDa
Source organism: Streptomyces coelicolor
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93J45 (Residues: 1-400; Coverage: 100%)
Gene names: SCBAC19G2.13c, SCO3058
Sequence domains: Membrane dipeptidase (Peptidase family M19)
Structure domains: Metal-dependent hydrolases

Ligands and Environments

2 bound ligands:
Ligand P8D 1 x P8D
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P3121
Unit cell:
a: 96.91Å b: 96.91Å c: 104.19Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.193 0.193 0.206
Expression system: Escherichia coli

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Citations

3 review citations

The Enzyme Function Initiative.
Gerlt et al. (2011)
2 more

1 mention without citation

Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase .
Cummings et al. (2010)