Crystal structure of the metallo-beta-lactamase imp-1 in complex with the bisthiazolidine inhibitor D-CS319

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 32% strand (DSSP).

Ligands and binding sites

• 3R9 · (3S,5S,7aR)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid · ligand · 5 copies · chains A, C, B, D
• ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
• NA · Sodium ion · metal · chains C
• CL · Chloride ion · ion · chains C
• EDO · 1,2-ethanediol · additive · 5 copies · chains B, A, C, D
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains B, C

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

Pockets

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

Interfaces

4 interfaces between chains.

• A–D · 740 Ų buried · 4 hydrogen bonds · protein-protein
• A–C · 538 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 437 Ų buried · 11 hydrogen bonds · protein-protein
• B–C · 33 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 5EV8 · Crystal structure of the metallo-beta-lactamase IMP-1 in complex with the bisthiazolidine… · the same entry in another collection · chain D against D, TM-score 1.00
• P52699 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (P52699) · a predicted model of the same protein · 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 P52699
• Elsewhere: RCSB PDB 5EV8 · PDBe 5EV8 · UniProt P52699