Crystal structure of new delhi metallo-beta-lactamase-1 in the complex with hydrolyzed meropenem

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).

Ligands and binding sites

• 0RV · (2S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-3-methyl-2H-pyrro le-5-carboxylic acid · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B
• ACY · Acetic acid · additive · 4 copies · chains A, B
• GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 753 Ų buried · 9 hydrogen bonds · protein-protein

Compared structures

• 4RBS · Crystal Structure of New Delhi Metallo-beta-Lactamase-1 in the Complex with Hydrolyzed… · the same entry in another collection · chain A against A, TM-score 1.00
• C7C422 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (C7C422) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 C7C422
• Elsewhere: RCSB PDB 4RBS · PDBe 4RBS · UniProt C7C422