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

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 14% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, D
• MAG · methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside · sugar · 2 copies · chains A, C, B, D
• ZN · Zinc ion · metal · 2 copies · chains A, C, B, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–B · 2347 Ų buried · 57 hydrogen bonds · protein-protein
• B–D · 355 Ų buried · 8 hydrogen bonds · protein-protein
• A–C · 355 Ų buried · 8 hydrogen bonds · protein-protein
• A–D · 78 Ų buried · 1 hydrogen bond · protein-protein
• B–C · 75 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 2 d-amino (nonstandard, D-amino acid).

Compared structures

• 4BXD · Crystal structure of AMPDH3 from pseudomonas aeruginosa in complex with tetrasaccharide… · 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 4BXD · PDBe 4BXD · UniProt Q9I5D1