Structure of the class D beta-lactamase oxa-1 in complex with doripenem

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).

Ligands and binding sites

• DRW · (2S,3R,4S)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A, B
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains 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, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 64 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified (covalent ligand, carboxylation).

Compared structures

• 3ISG · Structure of the class D beta-lactamase OXA-1 in complex with doripenem · the same entry in another collection · chain A against A, TM-score 1.00
• P13661 · AlphaFold monomer V2.0 prediction for beta-lactamase oxa-1 (P13661) · a predicted model of the same protein · chain A 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 P13661
• Elsewhere: RCSB PDB 3ISG · PDBe 3ISG · UniProt P13661