Research workbench
Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with uracil and phosphate ion at 2.49A resolution
Analyse Crystal 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
- 2RJ3
- Type
- protein
- Length
- 1,495 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
- URA, PO4
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 33% helix, 28% strand | P0A1F6 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 249 | 31% helix, 29% strand | P0A1F6 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 248 | 32% helix, 29% strand | P0A1F6 |
| F, E | Uridine phosphorylase (EC 2.4.2.3) | protein | 249 | 33% helix, 29% strand | P0A1F6 |
Ligands and binding sites
- URA · Uracil · ligand · 5 copies · chains A, D, F, E, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, F, C, E, D, B
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 | 445 | 0.74 | 0.83 | 55 | PO4, URA |
| 2 | 197 | 0.71 | 0.88 | 35 | PO4, URA |
| 3 | 484 | 0.70 | 0.80 | 53 | empty |
| 4 | 441 | 0.70 | 0.81 | 42 | empty |
| 5 | 408 | 0.70 | 0.81 | 37 | PO4 |
Interfaces
12 interfaces between chains.
- D–B · 2197 Ų buried · 24 hydrogen bonds · protein-protein
- A–F · 2166 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 2051 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 1060 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1038 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2RJ3 · Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex… · 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 2RJ3 · PDBe 2RJ3 · UniProt P0A1F6
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