Research workbench
Purine nucleoside phosphorylase from thermus thermophilus
Analyse Purine nucleoside phosphorylase from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ODK
- Type
- protein
- Length
- 1,384 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.28
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Purine nucleoside phosphorylase (EC 2.4.2.28) | protein | 228 | 39% helix, 30% strand | — |
| B, D, F | Purine nucleoside phosphorylase (EC 2.4.2.28) | protein | 234 | 38% helix, 29% strand | — |
| E | Purine nucleoside phosphorylase (EC 2.4.2.28) | protein | 226 | 39% helix, 30% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.75 | 0.83 | 53 | GOL |
| 2 | 549 | 0.75 | 0.83 | 49 | GOL |
| 3 | 672 | 0.75 | 0.81 | 53 | GOL |
| 4 | 58 | 0.71 | 0.98 | 20 | empty |
| 5 | 346 | 0.70 | 0.83 | 50 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1574 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1563 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1540 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1319 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1319 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1ODK · Purine nucleoside phosphorylase from thermus thermophilus · 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
- Elsewhere: RCSB PDB 1ODK · PDBe 1ODK
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