Crystal structure of inosine 5'-monophosphate dehydrogenase from clostridium perfringens complexed with imp and P221

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 23% strand (DSSP).

Ligands and binding sites

• IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
• 8N1 · N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-beta-D-xylofuranosylamine · ligand · 4 copies · chains A, D, B, C
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, D, B, C
• ACY · Acetic acid · additive · 3 copies · chains A, C, D
• FMT · Formic acid · additive · 2 copies · chains A, B, C, D
• MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B, C

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

Pockets

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

Interfaces

4 interfaces between chains.

• C–D · 2409 Ų buried · 39 hydrogen bonds · protein-protein
• B–C · 2301 Ų buried · 35 hydrogen bonds · protein-protein
• A–D · 2291 Ų buried · 36 hydrogen bonds · protein-protein
• A–B · 2188 Ų buried · 37 hydrogen bonds · protein-protein

Compared structures

• 5UZC · Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens… · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A0H2YRZ7
• Elsewhere: RCSB PDB 5UZC · PDBe 5UZC · UniProt A0A0H2YRZ7