Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S, 4R,5S)-3,4-dihydroxy-2-ethynyl-5-methylpyrrolidine

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).

Ligands and binding sites

• H79 · [(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-1-{3-[4-(3,4-dihydroxy-5-methylpyrrolidin-2-yl)-1H-1,2,3-triazol-1-yl]prop-1-en-1-yl}cyclopentadienyl]iron · ligand · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
• IMD · Imidazole · additive · 4 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 355 Ų buried · 1 hydrogen bond · protein-protein
• C–D · 339 Ų buried · 2 hydrogen bonds · protein-protein
• B–C · 101 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 5HDR · Crystal structure of a bacterial fucosidase with iminocyclitol… · 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 Q8A3I4
• Elsewhere: RCSB PDB 5HDR · PDBe 5HDR · UniProt Q8A3I4