Research workbench
Crystal structure of E. COLI purine nucleoside phosphorylase with PO4
Analyse Crystal structure of E. COLI purine nucleoside phosphorylase with PO4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OOE
- Type
- protein
- Length
- 1,393 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type
- EC
- 2.4.2.1
- UniProt
- C9QST6
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 36% helix, 29% strand | C9QST6 |
| C | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 225 | 38% helix, 28% strand | C9QST6 |
| D | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 230 | 37% helix, 29% strand | C9QST6 |
| E | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 227 | 36% helix, 30% strand | C9QST6 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 14 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.80 | 0.81 | 118 | PO4 |
| 2 | 233 | 0.69 | 0.86 | 45 | PO4 |
| 3 | 439 | 0.69 | 0.80 | 50 | PO4 |
| 4 | 50 | 0.68 | 0.97 | 21 | empty |
| 5 | 222 | 0.68 | 0.85 | 42 | PO4 |
Interfaces
12 interfaces between chains.
- B–D · 1779 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 1764 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1744 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 1738 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 1737 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3OOE · Crystal structure of E. Coli purine nucleoside phosphorylase with PO4 · 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 C9QST6
- Elsewhere: RCSB PDB 3OOE · PDBe 3OOE · UniProt C9QST6
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