Crystal structure of AMPDH3 from pseudomonas aeruginosa in complex with anhydromuramic pentapeptide

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 12% strand (DSSP).

Ligands and binding sites

• AH0 · 2-(2-acetylamino-4-hydroxy-6,8-dioxa-bicyclo[3.2.1]oct-3-yloxy)-propionic acid · ligand · 2 copies · chains A, C, B, D
• API · 2,6-diaminopimelic acid · ligand · 2 copies · chains A, B, C, D
• ACT · Acetate ion · additive · 3 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 2363 Ų buried · 53 hydrogen bonds · protein-protein
• A–C · 314 Ų buried · 7 hydrogen bonds · protein-protein
• B–D · 298 Ų buried · 6 hydrogen bonds · protein-protein
• B–C · 95 Ų buried · 0 hydrogen bonds · protein-protein
• A–D · 68 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 covalent, 6 d-amino (covalent ligand, D-amino acid).

Compared structures

• 4BXE · Crystal structure of AMPDH3 from pseudomonas aeruginosa in complex with anhydromuramic… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9I5D1
• Elsewhere: RCSB PDB 4BXE · PDBe 4BXE · UniProt Q9I5D1