Crystal structure of the lectin domain of the fimh variant ARG98ALA, in complex with methyl 3-chloro-4-D-mannopyranosyloxy-3- biphenylcarboxylate

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 53% strand (DSSP).

Ligands and binding sites

• SBQ · Methyl 3-[3-chloranyl-4-[(2~{R},3~{S},4~{S},5~{S}, 6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-phenyl]benzoate · ligand · 4 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D

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

Pockets

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

Interfaces

4 interfaces between chains.

• B–C · 321 Ų buried · 7 hydrogen bonds · protein-protein
• C–D · 113 Ų buried · 0 hydrogen bonds · protein-protein
• A–B · 113 Ų buried · 0 hydrogen bonds · protein-protein
• B–D · 55 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 7AYN · Crystal structure of the lectin domain of the FimH variant Arg98Ala, in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
• P08191 · AlphaFold monomer V2.0 prediction for type 1 fimbrin D-mannose specific adhesin (P08191) · a predicted model of the same protein · chain B against A, TM-score 0.83

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 P08191
• Elsewhere: RCSB PDB 7AYN · PDBe 7AYN · UniProt P08191