Crystal structure of CJ1430 in the presence of GDP-D-glycero-L-gluco- heptose, a GDP-D-glycero-4-keto-D-lyxo-heptose-3,5-epimerase from campylobacter jejuni

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 46% strand (DSSP).

Ligands and binding sites

• YO7 · [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl dihydrogen diphosphate (non-preferred name) · ligand · 6 copies · chains A, B, C, D, E, F
• EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D, E, F

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

Pockets

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

Interfaces

10 interfaces between chains.

• A–B · 1780 Ų buried · 35 hydrogen bonds · protein-protein
• E–F · 1763 Ų buried · 33 hydrogen bonds · protein-protein
• C–D · 1717 Ų buried · 32 hydrogen bonds · protein-protein
• B–C · 829 Ų buried · 21 hydrogen bonds · protein-protein
• C–F · 474 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 7M15 · crystal structure of cj1430 in the presence of GDP-D-glycero-L-gluco-heptose, a… · the same entry in another collection · chain B against B, 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 Q0P8I4
• Elsewhere: RCSB PDB 7M15 · PDBe 7M15 · UniProt Q0P8I4