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Crystal structure of uridine phosphorylase from schistosoma mansoni in complex with uracil
Analyse Crystal structure of uridine phosphorylase from schistosoma mansoni in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TXL
- 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
- URA, SO4
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 290 | 35% helix, 25% strand | G4VGI0 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 289 | 34% helix, 25% strand | G4VGI0 |
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 282 | 34% helix, 26% strand | G4VGI0 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 284 | 36% helix, 25% strand | G4VGI0 |
Ligands and binding sites
- URA · Uracil · ligand · 4 copies · chains C, D, A, B
- SO4 · Sulfate ion · ion · 4 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.77 | 0.83 | 103 | SO4, URA |
| 2 | 93 | 0.76 | 0.98 | 26 | SO4, URA |
| 3 | 90 | 0.76 | 0.98 | 26 | SO4, URA |
| 4 | 825 | 0.75 | 0.79 | 103 | empty |
| 5 | 72 | 0.73 | 0.98 | 26 | SO4, URA |
Interfaces
5 interfaces between chains.
- C–D · 2806 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2709 Ų buried · 30 hydrogen bonds · protein-protein
- C–B · 129 Ų buried · 2 hydrogen bonds · protein-protein
- D–B · 86 Ų buried · 0 hydrogen bonds · protein-protein
- C–A · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TXL · Crystal structure of uridine phosphorylase from Schistosoma mansoni in complex with uracil · the same entry in another collection · chain B against B, 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 4TXL · PDBe 4TXL · UniProt G4VGI0
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