Research workbench
Crystal structure of purine nucleoside phosphorylase with adenosine
Analyse Crystal structure of purine nucleoside phosphorylase with adenosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VHW
- Type
- protein
- Length
- 1,418 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- Q9KPM0
- Ligands
- ADN
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 237 | 37% helix, 28% strand | Q9KPM0 |
| E | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 236 | 37% helix, 28% strand | Q9KPM0 |
| F | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 234 | 36% helix, 28% strand | Q9KPM0 |
Ligands and binding sites
- ADN · Adenosine · ligand · 6 copies · chains A, D, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.83 | 0.84 | 116 | ADN |
| 2 | 336 | 0.65 | 0.80 | 52 | ADN |
| 3 | 320 | 0.64 | 0.80 | 52 | ADN |
| 4 | 281 | 0.64 | 0.81 | 48 | ADN |
| 5 | 339 | 0.63 | 0.79 | 55 | ADN |
Interfaces
12 interfaces between chains.
- B–D · 1814 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 1812 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 1806 Ų buried · 28 hydrogen bonds · protein-protein
- B–F · 1706 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 1706 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1VHW · Crystal structure of purine nucleoside phosphorylase with adenosine · the same entry in another collection · chain F against F, TM-score 1.00
- Q9KPM0 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type 1 (Q9KPM0) · a predicted model of the same protein · chain F 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 Q9KPM0
- Elsewhere: RCSB PDB 1VHW · PDBe 1VHW · UniProt Q9KPM0
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