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

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 29% strand (DSSP).

Ligands and binding sites

• ZZ7 · (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B
• SO4 · Sulfate ion · ion · 4 copies · chains A, B
• CL · Chloride ion · ion · chains A
• EDO · 1,2-ethanediol · additive · 3 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 · 913 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

• 5O2F · Crystal structure of NDM-1 in complex with hydrolyzed ampicillin - 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 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 5O2F · PDBe 5O2F · UniProt C7C422