Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispf) burkholderia pseudomallei in complex with ligand hgn- 0883

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 31% strand (DSSP).

Ligands and binding sites

• K4Y · 4-amino-N-(6-methoxypyrimidin-4-yl)benzene-1-sulfonamide · ligand · 3 copies · chains A, B, C
• ZN · Zinc ion · metal · 3 copies · chains A, B, C
• MG · Magnesium ion · metal · chains A, B, C
• DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, C
• MLA · Malonic acid · 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, 4 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 1123 Ų buried · 22 hydrogen bonds · protein-protein
• A–C · 1112 Ų buried · 21 hydrogen bonds · protein-protein
• B–C · 1111 Ų buried · 22 hydrogen bonds · protein-protein

Compared structures

• 6MWK · Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF)… · the same entry in another collection · chain A against A, TM-score 1.00
• Q3JRA0 · 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 0.98

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 Q3JRA0
• Elsewhere: RCSB PDB 6MWK · PDBe 6MWK · UniProt Q3JRA0