MolNFT v1 · #89865 · protein
X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with 5-fluorouracil at 2.15 a resolution
4E1V: “X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with 5-fluorouracil at…”. X-ray diffraction, 2 ligands (URF, K), 20 pockets (best druggability 0.76). MolNFT v1 #89865 on GenesisL1: 3D structure…
- PDB
- 4E1V
- Type
- protein
- Length
- 2,198 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- P0A1F6
- Ligands
- URF, K
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 248 | 28% helix, 29% strand | P0A1F6 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 31% helix, 30% strand | P0A1F6 |
| F, G | Uridine phosphorylase (EC 2.4.2.3) | protein | 242 | 31% helix, 30% strand | P0A1F6 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 31% helix, 30% strand | P0A1F6 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 246 | 29% helix, 30% strand | P0A1F6 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 244 | 32% helix, 30% strand | P0A1F6 |
| H | Uridine phosphorylase (EC 2.4.2.3) | protein | 243 | 30% helix, 30% strand | P0A1F6 |
| I | Uridine phosphorylase (EC 2.4.2.3) | protein | 243 | 30% helix, 30% strand | P0A1F6 |
Ligands and binding sites
- URF · 5-fluorouracil · ligand · 8 copies · chains A, E, F, D, C, B, H, G
- K · Potassium ion · metal · 3 copies · chains A, B, E, F, D, C
- GOL · Glycerol · additive · 5 copies · chains A, B, E, F, D, C
- EDO · 1,2-ethanediol · additive · chains D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.76 | 0.82 | 70 | empty |
| 2 | 425 | 0.69 | 0.81 | 47 | EDO |
| 3 | 222 | 0.69 | 0.86 | 35 | URF |
| 4 | 333 | 0.69 | 0.82 | 48 | URF, GOL |
| 5 | 238 | 0.69 | 0.85 | 42 | URF, GOL |
Interfaces
19 interfaces between chains.
- A–B · 2212 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2177 Ų buried · 21 hydrogen bonds · protein-protein
- D–C · 2173 Ų buried · 25 hydrogen bonds · protein-protein
- H–G · 2171 Ų buried · 27 hydrogen bonds · protein-protein
- E–D · 1027 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4E1V · X-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with… · 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 P0A1F6
- Elsewhere: RCSB PDB 4E1V · PDBe 4E1V · UniProt P0A1F6
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