1.55 a crystal structure of a ternary complex of GDP-mannose dehydrogenase from psuedomonas aeruginosa

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).

Ligands and binding sites

• NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
• GDX · Guanosine 5'-(trihydrogen diphosphate), P'-D-mannopyranosyl ester · ligand · 4 copies · chains A, B, C, D
• GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, D
• FRU · beta-D-fructofuranose · sugar · 2 copies · chains B, D
• ACY · Acetic acid · additive · 2 copies · chains C
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C

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

Pockets

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

Interfaces

6 interfaces between chains.

• A–B · 6188 Ų buried · 93 hydrogen bonds · protein-protein
• C–D · 6170 Ų buried · 87 hydrogen bonds · protein-protein
• A–C · 485 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 475 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 151 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 1MV8 · 1.55 A crystal structure of a ternary complex of GDP-mannose dehydrogenase from… · the same entry in another collection · chain D against D, TM-score 1.00
• P11759 · AlphaFold monomer V2.0 prediction for GDP-mannose 6-dehydrogenase (P11759) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P11759
• Elsewhere: RCSB PDB 1MV8 · PDBe 1MV8 · UniProt P11759