MolNFT v1 · #107026 · protein
Crystal structure of uridine phosphorylase from schistosoma mansoni in complex with thymidine
4TXJ: “Crystal structure of uridine phosphorylase from schistosoma mansoni in complex with thymidine”. X-ray diffraction, 2 ligands (THM, SO4), 16 pockets (best druggability 0.78). MolNFT v1 #107026 on GenesisL1: 3D structure, binding…
- PDB
- 4TXJ
- Type
- protein
- Length
- 1,161 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
- THM, SO4
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Uridine phosphorylase (EC 2.4.2.3) | protein | 290 | 34% helix, 25% strand | G4VGI0 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 291 | 34% helix, 25% strand | G4VGI0 |
Ligands and binding sites
- THM · Thymidine · 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
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.78 | 0.80 | 131 | empty |
| 2 | 92 | 0.76 | 0.98 | 28 | THM, SO4 |
| 3 | 87 | 0.76 | 0.98 | 25 | THM, SO4 |
| 4 | 93 | 0.75 | 0.97 | 27 | SO4, THM |
| 5 | 89 | 0.75 | 0.97 | 25 | THM, SO4 |
Interfaces
5 interfaces between chains.
- C–D · 2838 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2780 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 136 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 110 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TXJ · 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 4TXJ · PDBe 4TXJ · UniProt G4VGI0
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