Research workbench
X-ray structure of the unliganded uridine phosphorylase from yersinia pseudotuberculosis at 2.12A resolution
Analyse X-ray structure of the unliganded uridine phosphorylase from yersinia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I2V
- 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
- Q7AZX0
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 31% 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 | 31% helix, 24% strand | Q7AZX0 |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.74 | 0.78 | 82 | empty |
| 2 | 707 | 0.72 | 0.78 | 66 | empty |
| 3 | 395 | 0.69 | 0.81 | 39 | empty |
| 4 | 479 | 0.66 | 0.78 | 44 | empty |
| 5 | 420 | 0.65 | 0.79 | 36 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1901 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1886 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1845 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 360 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 151 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4I2V · X-ray structure of the unliganded uridine phosphorylase from Yersinia pseudotuberculosis… · 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 Q7AZX0
- Elsewhere: RCSB PDB 4I2V · PDBe 4I2V · UniProt Q7AZX0
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