MolNFT v1 · #58966 · protein
Crystal structure of trypanosoma brucei nucleoside phosphorylase shows uridine phosphorylase activity
3BJE · Nucleoside phosphorylase, putative: “Crystal structure of trypanosoma brucei nucleoside phosphorylase shows uridine phosphorylase activity”. X-ray diffraction, 3 ligands (R1P, URA, CA), 6 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 3BJE
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside phosphorylase, putative
- EC
- 2.4.2.-
- UniProt
- Q57VZ2
- Ligands
- R1P, URA, CA
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoside phosphorylase, putative (EC 2.4.2.-) | protein | 327 | 35% helix, 26% strand | Q57VZ2 |
Ligands and binding sites
- R1P · 1-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- URA · Uracil · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.70 | 0.85 | 35 | R1P, URA |
| 2 | 257 | 0.68 | 0.84 | 35 | R1P, URA |
| 3 | 76 | 0.39 | 0.78 | 21 | empty |
| 4 | 62 | 0.36 | 0.79 | 20 | empty |
| 5 | 84 | 0.35 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2939 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 3BJE · Crystal structure of Trypanosoma brucei nucleoside phosphorylase shows uridine… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q57VZ2
- Elsewhere: RCSB PDB 3BJE · PDBe 3BJE · UniProt Q57VZ2
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