MolNFT v1 · #50468 · protein
Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with uracil and phosphate ion at 2.49A resolution
2RJ3: “Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with uracil and…”. X-ray diffraction, 2 ligands (URA, PO4), 17 pockets (best druggability 0.74). MolNFT v1 #50468 on GenesisL1: 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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