Research workbench
Crystal structure of the uridine phosphorylase from salmonella typhimurium at 2.5A resolution
Analyse Crystal structure of the uridine phosphorylase from salmonella typhimurium at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SJ9
- Type
- protein
- Length
- 1,500 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
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 31% helix, 22% strand | P0A1F6 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.75 | 0.81 | 64 | empty |
| 2 | 570 | 0.73 | 0.81 | 49 | empty |
| 3 | 645 | 0.72 | 0.79 | 48 | empty |
| 4 | 511 | 0.71 | 0.80 | 58 | empty |
| 5 | 391 | 0.70 | 0.82 | 46 | empty |
Interfaces
12 interfaces between chains.
- B–D · 1852 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 1771 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 1728 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1058 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 1058 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1SJ9 · Crystal structure of the uridine phosphorylase from Salmonella typhimurium at 2.5A… · 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 1SJ9 · PDBe 1SJ9 · UniProt P0A1F6
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