Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4F-man

Structure

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

Ligands and binding sites

• G4F · [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl) oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R}, 3~{S},4~{R},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)-3,4-bis(oxidanyl)oxan-2-yl] hydrogen phosphate · ligand · 4 copies · chains A, D, C, B
• NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, D, C
• CIT · Citric acid · additive · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 2 copies · chains D, B, A

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• D–C · 1348 Ų buried · 19 hydrogen bonds · protein-protein
• A–B · 1329 Ų buried · 22 hydrogen bonds · protein-protein
• A–C · 1277 Ų buried · 13 hydrogen bonds · protein-protein
• D–B · 1273 Ų buried · 13 hydrogen bonds · protein-protein
• C–B · 356 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 6GPJ · Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4F-Man · 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 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 O60547
• Elsewhere: RCSB PDB 6GPJ · PDBe 6GPJ · UniProt O60547