Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei in complex with a fragment- nucleoside fusion D000161829

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 33% strand (DSSP).

Ligands and binding sites

• 829 · 5'-deoxy-5'-[(pyridin-4-ylcarbonyl)amino]cytidine · 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

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

Pockets

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

Interfaces

3 interfaces between chains.

• B–C · 1152 Ų buried · 25 hydrogen bonds · protein-protein
• A–B · 1119 Ų buried · 23 hydrogen bonds · protein-protein
• A–C · 1111 Ų buried · 23 hydrogen bonds · protein-protein

Compared structures

• 3KE1 · 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 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 Q63T71
• Elsewhere: RCSB PDB 3KE1 · PDBe 3KE1 · UniProt Q63T71