› 7ajz

X-ray diffraction
2.98Å resolution

The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with NAG-NAM(tetrapeptide)

Released:
DOI: 10.2210/pdb7ajz/pdb
PDB entry 7ajz coloured by chain, front view.
PDB entry 7ajz coloured by chain, side view.
PDB entry 7ajz coloured by chain, top view.
Source organisms:
Entry authors: Batuecas MT, Hermoso JA

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-167995 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L,D-TPase catalytic domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 523 amino acids
Theoretical weight: 59.86 KDa
Source organism: Vibrio cholerae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9KSI8 (Residues: 23-524; Coverage: 100%)
Gene name: VC_1268
Sequence domains:
NAG-NAM(tetrapeptide) Chain: C
Molecule details ›
Chain: C
Length: 4 amino acids
Theoretical weight: 461 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand EDO 2 x EDO
Ligand AMV 1 x AMV
3 modified residues:
Ligand DGL 1 x DGL
Ligand API 1 x API
Ligand DAL 1 x DAL

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P212121
Unit cell:
a: 57.51Å b: 92.558Å c: 276.064Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.21 0.266
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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