MolNFT v1 · #118011 · protein
X-ray structure of the complex pyrimidine-nucleoside phosphorylase from bacillus subtilis with sulfate ion
5EP8: “X-ray structure of the complex pyrimidine-nucleoside phosphorylase from bacillus subtilis with sulfate ion”. X-ray diffraction, 2 ligands (NA, SO4), 6 pockets (best druggability 0.73). MolNFT v1 #118011 on GenesisL1: 3D structure…
- PDB
- 5EP8
- Type
- protein
- Length
- 866 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrimidine-nucleoside phosphorylase
- EC
- 2.4.2.2
- UniProt
- P39142
- Ligands
- NA, SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyrimidine-nucleoside phosphorylase (EC 2.4.2.2) | protein | 433 | 47% helix, 16% strand | P39142 |
Ligands and binding sites
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 | 718 | 0.73 | 0.79 | 51 | SO4 |
| 2 | 670 | 0.70 | 0.78 | 56 | SO4 |
| 3 | 63 | 0.39 | 0.80 | 13 | empty |
| 4 | 93 | 0.38 | 0.76 | 19 | empty |
| 5 | 72 | 0.35 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 821 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5EP8 · X-Ray Structure of the Complex Pyrimidine-nucleoside phosphorylase from Bacillus subtilis… · the same entry in another collection · chain A against A, TM-score 1.00
- P39142 · AlphaFold monomer V2.0 prediction for pyrimidine-nucleoside phosphorylase (P39142) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P39142
- Elsewhere: RCSB PDB 5EP8 · PDBe 5EP8 · UniProt P39142
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