Atomic resolution X-ray crystal structure of a ruthenocene conjugated beta-lactam antibiotic in complex with ctx-M-14 S70G beta-lactamase

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).

Ligands and binding sites

• JSE · [(1,2,3,4,5-eta)-1-(4-{[carboxy(4-carboxy-5,5-dimethyl-1,3-thiazolidin-2-yl)methyl]amino}-4-oxobutanoyl) cyclopentadienyl][(1,2,3,4,5-eta)-cyclopentadienyl]ruthenium · ligand · 2 copies · chains A, B
• JSC · [(1,2,3,4,5-eta)-1-(4-{[carboxy(4-carboxy-5,5-dimethyl-1,3-thiazolidin-2-yl)methyl]amino}-4-oxobutanoyl) cyclopentadienyl][(1,2,3,4,5-eta)-cyclopentadienyl]ruthenium · ligand · chains A
• 7G4 · ruthenocene · ligand · chains B
• RU · Ruthenium ion · metal · 3 copies
• K · Potassium ion · metal · 2 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, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 119 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 modified (cyclization).

Compared structures

• 5TOP · Atomic Resolution X-Ray Crystal Structure of a Ruthenocene Conjugated Beta-Lactam… · 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 H6UQI0
• Elsewhere: RCSB PDB 5TOP · PDBe 5TOP · UniProt H6UQI0