Research workbench
Escherichia COLI purine nucleoside phosphorylase complexed with formycin B and PHOSPHATE/SULFATE
Analyse Escherichia COLI purine nucleoside phosphorylase complexed with formycin B and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PR1
- Type
- protein
- Length
- 700 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- P09743
- Ligands
- FMB, PO4
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 226 | 35% helix, 29% strand | P09743 |
| B, C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 237 | 36% helix, 28% strand | P09743 |
Ligands and binding sites
- FMB · Formycin B · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.59 | 0.77 | 52 | PO4, FMB |
| 2 | 267 | 0.58 | 0.78 | 39 | PO4, FMB |
| 3 | 194 | 0.50 | 0.77 | 37 | PO4, FMB |
| 4 | 119 | 0.37 | 0.73 | 18 | empty |
| 5 | 66 | 0.34 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 135 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 127 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 107 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1PR1 · Escherichia coli Purine Nucleoside Phosphorylase Complexed with Formycin B and… · 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 P09743
- Elsewhere: RCSB PDB 1PR1 · PDBe 1PR1 · UniProt P09743
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