Crystal structure of the metallo-beta-lactamase imp-1 in complex with the bisthiazolidine inhibitor L-VC26

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).

Ligands and binding sites

• 9BZ · (3~{R},5~{R},7~{a}~{S})-2,2-dimethyl-5-(sulfanylmethyl)-3,5,7,7~{a}-tetrahydro-[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid · ligand · 4 copies · chains A, D, B, C
• ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · chains A
• DMS · Dimethyl sulfoxide · additive · chains 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, 4 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–D · 732 Ų buried · 1 hydrogen bond · protein-protein
• A–C · 481 Ų buried · 5 hydrogen bonds · protein-protein
• A–B · 423 Ų buried · 9 hydrogen bonds · protein-protein
• B–C · 20 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 5EWA · 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 5EWA · PDBe 5EWA · UniProt P52699