MolNFT v1 · #107029 · protein
Crystal structure of uridine phosphorylase from schistosoma mansoni in complex with thymine
4TXM: “Crystal structure of uridine phosphorylase from schistosoma mansoni in complex with thymine”. X-ray diffraction, 2 ligands (TDR, SO4), 8 pockets (best druggability 0.75). MolNFT v1 #107029 on GenesisL1: 3D structure, binding sites…
- PDB
- 4TXM
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- G4VGI0
- Ligands
- TDR, SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 284 | 35% helix, 25% strand | G4VGI0 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 282 | 35% helix, 25% strand | G4VGI0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.75 | 0.98 | 27 | SO4, TDR |
| 2 | 674 | 0.75 | 0.81 | 90 | empty |
| 3 | 79 | 0.73 | 0.97 | 26 | SO4, TDR |
| 4 | 295 | 0.71 | 0.85 | 37 | empty |
| 5 | 52 | 0.41 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2749 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4TXM · Crystal structure of uridine phosphorylase from Schistosoma mansoni in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- G4VGI0 · AlphaFold monomer V2.0 prediction for uridine phosphorylase a (G4VGI0) · a predicted model of the same protein · chain B 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 4TXM · PDBe 4TXM · UniProt G4VGI0
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