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Uridine phosphorylase from salmonella typhimurium. crystal structure at 2.9 a resolution
Analyse Uridine phosphorylase from salmonella typhimurium. crystal structure at 2.9 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RYZ
- 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
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 30% helix, 24% strand | P0A1F6 |
Ligands and binding sites
- ACY · Acetic acid · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.74 | 0.77 | 80 | empty |
| 2 | 446 | 0.73 | 0.83 | 40 | empty |
| 3 | 495 | 0.72 | 0.81 | 42 | empty |
| 4 | 544 | 0.69 | 0.79 | 51 | empty |
| 5 | 308 | 0.68 | 0.82 | 35 | empty |
Interfaces
9 interfaces between chains.
- B–D · 1923 Ų buried · 31 hydrogen bonds · protein-protein
- A–F · 1869 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 1768 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1011 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 212 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1RYZ · Uridine Phosphorylase from Salmonella typhimurium. Crystal Structure at 2.9 A Resolution · the same entry in another collection · chain C against C, TM-score 1.00
- P0A1F6 · AlphaFold monomer V2.0 prediction for uridine phosphorylase (P0A1F6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 1RYZ · PDBe 1RYZ · UniProt P0A1F6
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