Research workbench
Crystal structure of purine nucleoside phosphorylase in complex with ribose-1-phosphate
Analyse Crystal structure of purine nucleoside phosphorylase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FB1
- Type
- protein
- Length
- 836 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
- Q9BMI9
- Ligands
- R1P
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 281 | 36% helix, 23% strand | Q9BMI9 |
| B | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 270 | 34% helix, 24% strand | Q9BMI9 |
| C | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 285 | 35% helix, 24% strand | Q9BMI9 |
Ligands and binding sites
- R1P · 1-O-phosphono-alpha-D-ribofuranose · ligand · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.73 | 0.99 | 24 | empty |
| 2 | 68 | 0.70 | 0.96 | 21 | R1P, ACT |
| 3 | 60 | 0.68 | 0.96 | 20 | R1P, ACT |
| 4 | 226 | 0.53 | 0.77 | 34 | R1P, ACT |
| 5 | 211 | 0.50 | 0.76 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1270 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1270 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1147 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3FB1 · Crystal Structure of Purine Nucleoside Phosphorylase in Complex with Ribose-1-Phosphate · 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 Q9BMI9
- Elsewhere: RCSB PDB 3FB1 · PDBe 3FB1 · UniProt Q9BMI9
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