MolNFT v1 · #74160 · protein
Crystal structure of E. COLI purine nucleoside phosphorylase with PO4
3OOH · Purine nucleoside phosphorylase deod-type: “Crystal structure of E. COLI purine nucleoside phosphorylase with PO4”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.84). MolNFT v1 #74160 on GenesisL1: 3D structure…
- PDB
- 3OOH
- Type
- protein
- Length
- 4,266 residues
- Chains
- 18
- 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
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 35% helix, 29% strand | C9QST6 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 23 copies · chains A, D, B, E, C, F, G, J, H, K, M, I, L, P, N, Q, O, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.84 | 0.85 | 159 | PO4 |
| 2 | 724 | 0.83 | 0.87 | 107 | PO4 |
| 3 | 835 | 0.82 | 0.85 | 87 | PO4 |
| 4 | 836 | 0.82 | 0.84 | 113 | PO4 |
| 5 | 829 | 0.81 | 0.84 | 79 | empty |
Interfaces
56 interfaces between chains.
- A–F · 1771 Ų buried · 24 hydrogen bonds · protein-protein
- I–K · 1767 Ų buried · 29 hydrogen bonds · protein-protein
- O–Q · 1766 Ų buried · 25 hydrogen bonds · protein-protein
- H–J · 1762 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 1758 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3OOH · 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 3OOH · PDBe 3OOH · UniProt C9QST6
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