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

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).

Ligands and binding sites

• 3S0 · (2R,5S)-5-[(carbamoyloxy)methyl]-2-[(R)-carboxy{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}methyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B
• UNL · Unknown ligand · ion · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · chains A

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 · 812 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 5O2E · Crystal structure of NDM-1 in complex with hydrolyzed cefuroxime - 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 0.96

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 5O2E · PDBe 5O2E · UniProt C7C422