Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei with bound CTP and cdp

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 32% strand (DSSP).

Ligands and binding sites

• CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains A, C, B
• CTP · Cytidine-5'-triphosphate · ligand · chains A, B
• ZN · Zinc ion · metal · 3 copies · chains A, B, C
• GOL · Glycerol · additive · chains A, B, 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 · 1157 Ų buried · 26 hydrogen bonds · protein-protein
• A–B · 1157 Ų buried · 21 hydrogen bonds · protein-protein
• A–C · 1110 Ų buried · 21 hydrogen bonds · protein-protein

Compared structures

• 3IEW · 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 3IEW · PDBe 3IEW · UniProt Q63T71