MolNFT v1 · #136579 · protein
Crystal structure of inosine 5'-monophosphate dehydrogenase from clostridium perfringens complexed with imp and P178
5UXE · Inosine-5'-monophosphate dehydrogenase: “Crystal structure of inosine 5'-monophosphate dehydrogenase from clostridium perfringens complexed with imp…”. X-ray diffraction, 4 ligands (IMP, 8LA, K), 17 pockets (best druggability 0.80).…
- PDB
- 5UXE
- Type
- protein
- Length
- 1,374 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate dehydrogenase
- EC
- 1.1.1.205
- UniProt
- A0A127ELD1
- Ligands
- IMP, 8LA, K, SO4
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 343 | 37% helix, 24% strand | A0A127ELD1 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 346 | 37% helix, 24% strand | A0A127ELD1 |
| D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 342 | 38% helix, 23% strand | A0A127ELD1 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
- 8LA · N-[4-chloro-3-(alpha-D-ribofuranosyloxy)phenyl]-N'-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea · ligand · 4 copies · chains A, C, B, D
- K · Potassium ion · metal · 3 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · chains C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, D
- FMT · Formic acid · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.80 | 0.82 | 84 | IMP, 8LA |
| 2 | 924 | 0.80 | 0.82 | 89 | IMP, 8LA |
| 3 | 751 | 0.78 | 0.82 | 69 | IMP, 8LA |
| 4 | 705 | 0.77 | 0.82 | 64 | IMP, 8LA |
| 5 | 476 | 0.69 | 0.80 | 44 | FMT |
Interfaces
4 interfaces between chains.
- A–B · 2403 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 2324 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2322 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2308 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 5UXE · 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 A0A127ELD1
- Elsewhere: RCSB PDB 5UXE · PDBe 5UXE · UniProt A0A127ELD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.