Crystal structure of ndm-1 in complex with hydrolyzed meropenem - new refinement

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 28% strand (DSSP).

Ligands and binding sites

• 8YL · (2S,3R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3S,5S)-5-(dimethylcarbamoyl) pyrrolidin-3-yl]sulfan yl-3-methyl-2,3-dihydro-1H-pyrrole-5-carboxylic acid · ligand · chains A
• ZN · Zinc ion · metal · 4 copies · chains A, B
• SO4 · Sulfate ion · ion · chains A
• GOL · Glycerol · additive · 5 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 948 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 5N0H · Crystal structure of NDM-1 in complex with hydrolyzed meropenem - new refinement · 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 0.97

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 5N0H · PDBe 5N0H · UniProt C7C422