Crystal structure of metallo-beta-lactamase smb-1 bound to hydrolyzed doripenem

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).

Ligands and binding sites

• DQM · (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-methyl-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid · ligand · chains A
• NA · Sodium ion · metal · 7 copies · chains A
• ZN · Zinc ion · metal · 2 copies · chains A
• SO4 · Sulfate ion · ion · 3 copies · chains A

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.

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 5B15 · Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Doripenem · 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 G5ELM3
• Elsewhere: RCSB PDB 5B15 · PDBe 5B15 · UniProt G5ELM3