Structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with a cdp derived fluorescent inhibitor

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 29% strand (DSSP).

Ligands and binding sites

• 1AA · 5'-O-[({[(2-{[(2-aminophenyl)carbonyl]oxy}ethyl) oxy]phosphinato}oxy)phosphinato]cytidine · ligand · 6 copies · chains A, B, C, D, F, E
• GPP · Geranyl diphosphate · ligand · 2 copies · chains A, B, C, F, D, E
• ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

12 interfaces between chains.

• B–C · 1066 Ų buried · 20 hydrogen bonds · protein-protein
• A–B · 1040 Ų buried · 17 hydrogen bonds · protein-protein
• A–C · 1035 Ų buried · 16 hydrogen bonds · protein-protein
• D–F · 1017 Ų buried · 19 hydrogen bonds · protein-protein
• D–E · 1011 Ų buried · 16 hydrogen bonds · protein-protein

Compared structures

• 2AMT · Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase complexed with a CDP… · the same entry in another collection · chain C against C, 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 0.97

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 2AMT · PDBe 2AMT · UniProt P62617