Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei with fol fragment 535, ethyl 3-methyl-5,6-DIHYDROIMIDAZO[2,1-B][1,3]THIAZOLE-2-carboxylate

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 31% strand (DSSP).

Ligands and binding sites

• 535 · ethyl 3-methyl-5,6-dihydroimidazo[2,1-b][1,3]thiazole-2-carboxylate · ligand · 3 copies · chains A, B, C
• ZN · Zinc ion · metal · 3 copies · chains A, B, C
• K · Potassium ion · metal · chains A, B, C
• CL · Chloride ion · ion · chains A
• ACT · Acetate ion · additive · chains A, C

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–C · 1152 Ų buried · 23 hydrogen bonds · protein-protein
• A–B · 1109 Ų buried · 22 hydrogen bonds · protein-protein
• A–C · 1098 Ų buried · 23 hydrogen bonds · protein-protein

Compared structures

• 3K14 · Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from… · the same entry in another collection · chain A against A, TM-score 1.00
• Q63T71 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · a predicted model of the same protein · chain C 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 Q63T71
• Elsewhere: RCSB PDB 3K14 · PDBe 3K14 · UniProt Q63T71