High resolution structure of acinetobacter baumannii beta-lactamase oxa-51 I129L/K83D bound to doripenem

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).

Ligands and binding sites

• 4J6 · (4R,5S)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-3-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
• GOL · Glycerol · additive · 6 copies · chains A, B, C, D
• ACT · Acetate ion · additive · 3 copies · chains A, C, D

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–D · 452 Ų buried · 4 hydrogen bonds · protein-protein
• C–D · 405 Ų buried · 3 hydrogen bonds · protein-protein
• A–B · 396 Ų buried · 4 hydrogen bonds · protein-protein
• A–C · 376 Ų buried · 7 hydrogen bonds · protein-protein
• B–D · 354 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 5L2F · High Resolution Structure of Acinetobacter baumannii beta-lactamase OXA-51 I129L/K83D… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q5QT35
• Elsewhere: RCSB PDB 5L2F · PDBe 5L2F · UniProt Q5QT35