Crystal structure of human alpha-L-iduronidase complex with 2-deoxy-2- fluoro-alpha-L-idopyranosyluronic acid fluoride

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).

Ligands and binding sites

• FIF · 2,6-anhydro-5-deoxy-5-fluoro-L-idonic acid · ligand · 2 copies · chains A, B
• SRT · S,R meso-tartaric acid · ligand · chains B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 6 copies · chains A, B
• TLA · L(+)-tartaric acid · additive · chains B

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 299 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 glycan, 2 covalent (N-glycosylation, covalent ligand).

Compared structures

• 4KH2 · Crystal structure of human alpha-L-iduronidase complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• P35475 · AlphaFold monomer V2.0 prediction for alpha-L-iduronidase (P35475) · a predicted model of the same protein · chain B 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 P35475
• Elsewhere: RCSB PDB 4KH2 · PDBe 4KH2 · UniProt P35475