Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei with cytidine and FOL694, 2- (thiophen-2-YL)PHENYL methanol

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 33% strand (DSSP).

Ligands and binding sites

• CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 3 copies · chains A, C, B
• F69 · (2-thiophen-2-ylphenyl)methanol · ligand · chains A
• ZN · Zinc ion · metal · 3 copies · chains A, B, C
• K · Potassium ion · metal · chains A, B, C
• CL · Chloride ion · ion · chains A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 1167 Ų buried · 23 hydrogen bonds · protein-protein
• B–C · 1152 Ų buried · 22 hydrogen bonds · protein-protein
• A–C · 1113 Ų buried · 21 hydrogen bonds · protein-protein

Compared structures

• 3P10 · Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from… · the same entry in another collection · chain A against A, TM-score 1.00
• Q3JRA0 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · a predicted model of the same protein · chain A 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 Q3JRA0
• Elsewhere: RCSB PDB 3P10 · PDBe 3P10 · UniProt Q3JRA0