Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 32% strand (DSSP).

Ligands and binding sites

• C6B · [(2S,3S,4R,5S)-5-(4-amino-2-oxo-pyrimidin-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate · ligand · chains A
• GPP · Geranyl diphosphate · ligand · chains A
• ZN · Zinc ion · metal · chains A
• GOL · Glycerol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Compared structures

• 3FBA · Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
• P62617 · 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 0.96

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 P62617
• Elsewhere: RCSB PDB 3FBA · PDBe 3FBA · UniProt P62617