Research workbench
Crystal structure of uridine phosphorylase from schistosoma mansoni in apo form
Analyse Crystal structure of uridine phosphorylase from schistosoma mansoni in apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TXH
- Type
- protein
- Length
- 1,145 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- G4VGI0
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 289 | 35% helix, 25% strand | G4VGI0 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 290 | 34% helix, 25% strand | G4VGI0 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 286 | 35% helix, 25% strand | G4VGI0 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 280 | 31% helix, 24% strand | G4VGI0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.80 | 0.81 | 132 | empty |
| 2 | 100 | 0.77 | 0.98 | 27 | empty |
| 3 | 99 | 0.76 | 0.97 | 27 | SO4 |
| 4 | 99 | 0.76 | 0.97 | 27 | SO4 |
| 5 | 675 | 0.75 | 0.81 | 89 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2763 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2604 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 159 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TXH · Crystal structure of uridine phosphorylase from Schistosoma mansoni in APO form · the same entry in another collection · chain D against D, TM-score 1.00
- G4VGI0 · AlphaFold monomer V2.0 prediction for uridine phosphorylase a (G4VGI0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 G4VGI0
- Elsewhere: RCSB PDB 4TXH · PDBe 4TXH · UniProt G4VGI0
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