› 2zdh

X-ray diffraction
1.9Å resolution

Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8

Released:
DOI: 10.2210/pdb2zdh/pdb
PDB entry 2zdh coloured by chain, front view.
PDB entry 2zdh coloured by chain, side view.
PDB entry 2zdh coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Entry authors: Kitamuta Y, Yokoyama S, Kuramitsu S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reaction catalysed: 
ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177919 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanine--D-alanine ligase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 319 amino acids
Theoretical weight: 34.7 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SHZ3 (Residues: 1-319; Coverage: 100%)
Gene names: TTHA1587, ddl
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MG 7 x MG
Ligand ADP 4 x ADP
Ligand DAL 2 x DAL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P212121
Unit cell:
a: 68.946Å b: 105.394Å c: 199.748Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.207 0.239
Expression system: Escherichia coli BL21(DE3)

Quick links