Crystal structure of ndm-1 with vnrx-5133

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).

Ligands and binding sites

• K9K · (10AR)-2-(((1R,4R)-4-((2-aminoethyl)amino)cyclohexyl) methyl)-6-carboxy-4-hydroxy-4,10A-dihydro-10H-benzo[5, 6][1,2]oxaborinino[2,3-b][1,4,2]oxazaborol-4-uide · ligand · 2 copies · chains A, B
• K9B · (4~{R})-4-[2-[4-(2-azanylethylamino) cyclohexyl]ethanoylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid · ligand · chains A
• ZN · Zinc ion · metal · 4 copies · chains A, B
• SO4 · Sulfate ion · ion · 3 copies · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 912 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 6RMF · Crystal structure of NDM-1 with VNRX-5133 · 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 0.99

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 6RMF · PDBe 6RMF · UniProt C7C422