PDBe 2yzm

X-ray diffraction
2.21Å resolution

Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8

Source organism: Thermus thermophilus HB8
Entry authors: Kitamura Y, Yokoyama S, Kuramitsu S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Structure analysis Details

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

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: C2
Unit cell:
a: 166.705Å b: 55.849Å c: 141.387Å
α: 90° β: 109.34° γ: 90°
R R work R free
0.224 0.224 0.266
Expression system: Escherichia coli