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X-ray structure of uridine phosphorylase from yersinia pseudotuberculosis in unliganded state at 2.27 a resolution
Analyse X-ray structure of uridine phosphorylase from yersinia pseudotuberculosis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JP5
- Type
- protein
- Length
- 1,441 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- Q8D1I4
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 240 | 32% helix, 30% strand | Q8D1I4 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 241 | 29% helix, 31% strand | Q8D1I4 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 239 | 31% helix, 27% strand | Q8D1I4 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 239 | 31% helix, 31% strand | Q8D1I4 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 243 | 30% helix, 28% strand | Q8D1I4 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 239 | 30% helix, 30% strand | Q8D1I4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, E, F
- GOL · Glycerol · additive · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.73 | 0.81 | 88 | EDO |
| 2 | 370 | 0.70 | 0.82 | 43 | empty |
| 3 | 347 | 0.66 | 0.81 | 42 | empty |
| 4 | 286 | 0.66 | 0.82 | 35 | empty |
| 5 | 262 | 0.66 | 0.82 | 31 | empty |
Interfaces
12 interfaces between chains.
- D–F · 1945 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1930 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1926 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1018 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1016 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4JP5 · X-ray structure of uridine phosphorylase from Yersinia pseudotuberculosis in unliganded… · 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 Q8D1I4
- Elsewhere: RCSB PDB 4JP5 · PDBe 4JP5 · UniProt Q8D1I4
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