MolNFT v1 · #136356 · protein
Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from campylobacter jejuni in the complex with imp and the inhibitor P225
5UQF · Inosine-5'-monophosphate dehydrogenase: “Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from campylobacter…”. X-ray diffraction, 5 ligands (IMP, 8KY, K), 15 pockets (best druggability 0.76).…
- PDB
- 5UQF
- Type
- protein
- Length
- 1,064 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate dehydrogenase
- EC
- 1.1.1.205
- UniProt
- A0A1B3XFT6, A5KFK9
- Ligands
- IMP, 8KY, K, SO4, CL
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 354 | 36% helix, 20% strand | A0A1B3XFT6, A5KFK9 |
| B, C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 355 | 34% helix, 19% strand | A0A1B3XFT6, A5KFK9 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 3 copies · chains A, B, C
- 8KY · {2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenoxy}acetic acid · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.76 | 0.82 | 59 | IMP |
| 2 | 452 | 0.75 | 0.84 | 47 | IMP, EDO |
| 3 | 430 | 0.74 | 0.84 | 48 | IMP, 8KY |
| 4 | 275 | 0.58 | 0.77 | 25 | empty |
| 5 | 254 | 0.56 | 0.77 | 25 | EDO |
Interfaces
1 interface between chains.
- B–C · 91 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5UQF · Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from… · 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 A0A1B3XFT6
- Every structure of UniProt A5KFK9
- Elsewhere: RCSB PDB 5UQF · PDBe 5UQF · UniProt A0A1B3XFT6 · UniProt A5KFK9
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