Structural and mechanistic insights into ndm-1 catalyzed hydrolysis of cephalosporins

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 31% strand (DSSP).

Ligands and binding sites

• 3S3 · (1R)-2-({(R)-carboxy[(2R,5S)-4-carboxy-5-methyl-5,6-dihydro-2H-1,3-thiazin-2-yl]methyl}amino)-2-oxo-1-phenylethanaminium · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 916 Ų buried · 8 hydrogen bonds · protein-protein

Compared structures

• 4RL2 · Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins · the same entry in another collection · chain B against B, 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 B against A, TM-score 0.94

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 4RL2 · PDBe 4RL2 · UniProt C7C422