Research workbench
X-ray structure of unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.4 A resolution
Analyse X-ray structure of 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
- 4OF4
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- Yersinia pseudotuberculosis
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- Q7AZX0
- Ligands
- NA
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.4 · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 32% helix, 28% strand | Q7AZX0 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.73 | 0.82 | 49 | EDO |
| 2 | 489 | 0.71 | 0.81 | 50 | empty |
| 3 | 78 | 0.31 | 0.73 | 21 | EDO |
| 4 | 83 | 0.31 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2080 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4OF4 · X-ray structure of unliganded uridine phosphorylase from yersinia pseudotuberculosis at… · 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 4OF4 · PDBe 4OF4 · UniProt Q7AZX0
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