Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphorylated D-cycloserine, MG2+ and K+

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).

Ligands and binding sites

• ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
• DS0 · [(4R)-4-azanyl-4,5-dihydro-1,2-oxazol-3-yl] dihydrogen phosphate · ligand · chains C
• MG · Magnesium ion · metal · 2 copies · chains C
• K · Potassium ion · metal · chains C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• C–D · 1585 Ų buried · 7 hydrogen bonds · protein-protein
• A–B · 1441 Ų buried · 6 hydrogen bonds · protein-protein
• B–C · 291 Ų buried · 1 hydrogen bond · protein-protein
• B–D · 142 Ų buried · 1 hydrogen bond · protein-protein
• A–C · 31 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 6U1I · Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphorylated… · the same entry in another collection · chain D against D, TM-score 1.00
• Q5SHZ3 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q5SHZ3) · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q5SHZ3
• Elsewhere: RCSB PDB 6U1I · PDBe 6U1I · UniProt Q5SHZ3