MolNFT v1 · #107030 · protein
Crystal structure of uridine phosphorylase from schistosoma mansoni in complex with 5-fluorouracil
4TXN: “Crystal structure of uridine phosphorylase from schistosoma mansoni in complex with 5-fluorouracil”. X-ray diffraction, 2 ligands (URF, SO4), 12 pockets (best druggability 0.77). MolNFT v1 #107030 on GenesisL1: 3D structure, binding…
- PDB
- 4TXN
- Type
- protein
- Length
- 1,153 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
- URF, SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 287 | 36% helix, 24% strand | G4VGI0 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 286 | 36% helix, 25% strand | G4VGI0 |
| C, D | Uridine phosphorylase (EC 2.4.2.3) | protein | 290 | 35% helix, 25% strand | G4VGI0 |
Ligands and binding sites
- URF · 5-fluorouracil · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.77 | 0.94 | 39 | SO4, URF |
| 2 | 587 | 0.77 | 0.83 | 81 | SO4, URF |
| 3 | 458 | 0.75 | 0.84 | 70 | SO4, URF |
| 4 | 85 | 0.75 | 0.97 | 27 | SO4, URF |
| 5 | 284 | 0.72 | 0.85 | 43 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2825 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2797 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 55 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TXN · 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 4TXN · PDBe 4TXN · UniProt G4VGI0
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