Research workbench
X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with by phosphate ion at 1.5A resolution
Analyse X-ray structure of the uridine phosphorylase from salmonella typhimurium in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DDO
- Type
- protein
- Length
- 1,469 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- P0A1F6
- Ligands
- PO4
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 240 | 32% helix, 28% strand | P0A1F6 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 244 | 32% helix, 30% strand | P0A1F6 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 249 | 34% helix, 27% strand | P0A1F6 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 33% helix, 29% strand | P0A1F6 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 242 | 34% helix, 29% strand | P0A1F6 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 243 | 33% helix, 30% strand | P0A1F6 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, F, B, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.75 | 0.82 | 75 | empty |
| 2 | 476 | 0.71 | 0.81 | 58 | empty |
| 3 | 425 | 0.70 | 0.81 | 37 | empty |
| 4 | 439 | 0.68 | 0.80 | 37 | PO4 |
| 5 | 362 | 0.67 | 0.81 | 44 | PO4 |
Interfaces
12 interfaces between chains.
- B–D · 2088 Ų buried · 24 hydrogen bonds · protein-protein
- A–F · 2055 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 2037 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 1038 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1029 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3DDO · 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 3DDO · PDBe 3DDO · UniProt P0A1F6
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