Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4K6D-man

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).

Ligands and binding sites

• F7E · [[(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},6~{R})-6-methyl-3,4-bis(oxidanyl)-5-oxidanylidene-oxan-2-yl] hydrogen phosphate · ligand · 4 copies · chains B, C, D, E
• NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains B, E, C, D
• BCN · Bicine · ligand · chains B, E
• EDO · 1,2-ethanediol · additive · 9 copies · chains B, C, E, D

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

Pockets

12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• C–D · 1299 Ų buried · 20 hydrogen bonds · protein-protein
• D–E · 1283 Ų buried · 12 hydrogen bonds · protein-protein
• B–E · 1252 Ų buried · 19 hydrogen bonds · protein-protein
• B–C · 1248 Ų buried · 12 hydrogen bonds · protein-protein
• B–D · 277 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 6GPL · Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4k6d-Man · the same entry in another collection · chain B against B, 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 E 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 6GPL · PDBe 6GPL · UniProt O60547