Co-crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from cryptosporidium parvum and the inhibitor P131

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).

Ligands and binding sites

• IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
• I13 · 1-(2-{3-[(1E)-N-(2-aminoethoxy)ethanimidoyl]phenyl}propan-2-yl)-3-(4-chloro-3-nitrophenyl)urea · ligand · 4 copies · chains A, D, B, C
• GOL · Glycerol · additive · 4 copies · chains A, B, C, D
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D, B

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

Pockets

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 1866 Ų buried · 31 hydrogen bonds · protein-protein
• C–D · 1854 Ų buried · 29 hydrogen bonds · protein-protein
• A–D · 1844 Ų buried · 31 hydrogen bonds · protein-protein
• B–C · 1812 Ų buried · 27 hydrogen bonds · protein-protein
• B–D · 24 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

• 4RV8 · Co-Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase… · the same entry in another collection · chain A against A, TM-score 1.00
• Q8T6T2 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase (Q8T6T2) · 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 Q8T6T2
• Elsewhere: RCSB PDB 4RV8 · PDBe 4RV8 · UniProt Q8T6T2