MolNFT v1 · #136638 · protein
Crystal structure of inosine 5'-monophosphate dehydrogenase from clostridium perfringens complexed with imp and P182
5UZE · Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'…: “Crystal structure of inosine 5'-monophosphate dehydrogenase from clostridium perfringens complexed with imp…”. X-ray diffraction, 3 ligands (IMP, 8L1, K), 12 pockets (best…
- PDB
- 5UZE
- Type
- protein
- Length
- 1,367 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase
- EC
- 1.1.1.205
- UniProt
- A0A0H2YRZ7
- Ligands
- IMP, 8L1, K
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 341 | 38% helix, 22% strand | A0A0H2YRZ7 |
| B | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 343 | 37% helix, 23% strand | A0A0H2YRZ7 |
| C | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 341 | 37% helix, 22% strand | A0A0H2YRZ7 |
| D | Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205) | protein | 342 | 38% helix, 22% strand | A0A0H2YRZ7 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
- 8L1 · N-{4-chloro-3-[4-(trifluoromethyl)-1,3-thiazol-2-yl]phenyl}-N'-(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)urea · ligand · 4 copies · chains A, C, B, D
- K · Potassium ion · metal · 2 copies · chains A, B, D
- GOL · Glycerol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.79 | 0.82 | 84 | IMP, 8L1 |
| 2 | 985 | 0.79 | 0.81 | 86 | IMP, 8L1 |
| 3 | 1033 | 0.79 | 0.80 | 85 | IMP, 8L1 |
| 4 | 746 | 0.78 | 0.82 | 66 | IMP, 8L1 |
| 5 | 588 | 0.69 | 0.78 | 44 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2278 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2260 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 2252 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2234 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5UZE · 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 5UZE · PDBe 5UZE · UniProt A0A0H2YRZ7
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