Leca from pseudomonas aeruginosa in complex with a synthetic monovalent galactosidic inhibitor

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 45% strand (DSSP).

Ligands and binding sites

• 4VH · N-[2-[4-[(2S)-3-(2-hydroxyethylamino)-3-oxidanylidene-2-(2-phenoxyethanoylamino)propyl]-1,2,3-triazol-1-yl]ethyl]-4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanyl-benzamide · ligand · 4 copies · chains A, B, C, D
• CA · Calcium ion · metal · 4 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 3 copies · chains A, C, D

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 1076 Ų buried · 14 hydrogen bonds · protein-protein
• C–D · 990 Ų buried · 10 hydrogen bonds · protein-protein
• B–C · 393 Ų buried · 8 hydrogen bonds · protein-protein
• A–D · 349 Ų buried · 8 hydrogen bonds · protein-protein
• A–C · 250 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 7FIO · LecA from Pseudomonas aeruginosa in complex with a synthetic monovalent galactosidic… · the same entry in another collection · chain A against A, TM-score 1.00
• Q05097 · AlphaFold monomer V2.0 prediction for pa-I galactophilic lectin (Q05097) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q05097
• Elsewhere: RCSB PDB 7FIO · PDBe 7FIO · UniProt Q05097