Crystal structure of GDP-mannose 4,6 dehydratase bound to a GDP-fucose based inhibitor

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).

Ligands and binding sites

• NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
• GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
• 6CK · [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5S,6R)-3,4,5-trihydroxy-6-(trifluoromethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name) · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Interfaces

6 interfaces between chains.

• C–D · 1840 Ų buried · 31 hydrogen bonds · protein-protein
• A–B · 1830 Ų buried · 28 hydrogen bonds · protein-protein
• A–C · 1258 Ų buried · 12 hydrogen bonds · protein-protein
• B–D · 1228 Ų buried · 10 hydrogen bonds · protein-protein
• A–D · 304 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 5IN4 · Crystal Structure of GDP-mannose 4,6 dehydratase bound to a GDP-fucose based inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
• O60547 · AlphaFold monomer V2.0 prediction for GDP-mannose 4,6 dehydratase (O60547) · 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 O60547
• Elsewhere: RCSB PDB 5IN4 · PDBe 5IN4 · UniProt O60547