Research workbench
Crystal structure of E. COLI purine nucleoside phosphorylase ARG24ALA mutant
Analyse Crystal structure of E. COLI purine nucleoside phosphorylase ARG24ALA mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OPV
- Type
- protein
- Length
- 2,835 residues
- Chains
- 12
- 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 · 3 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G, H, I, K, L | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 35% helix, 28% strand | C9QST6 |
| E | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 232 | 36% helix, 29% strand | C9QST6 |
| J | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 233 | 37% helix, 28% strand | C9QST6 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 14 copies · chains A, D, B, E, C, F, G, J, H, K, I, L
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 | 1158 | 0.84 | 0.85 | 114 | PO4 |
| 2 | 950 | 0.82 | 0.84 | 87 | PO4 |
| 3 | 478 | 0.78 | 0.86 | 61 | empty |
| 4 | 290 | 0.75 | 0.87 | 51 | PO4 |
| 5 | 800 | 0.73 | 0.78 | 66 | PO4 |
Interfaces
34 interfaces between chains.
- B–D · 1776 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 1773 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 1767 Ų buried · 26 hydrogen bonds · protein-protein
- H–J · 1766 Ų buried · 22 hydrogen bonds · protein-protein
- I–K · 1763 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3OPV · Crystal structure of E. Coli purine nucleoside phosphorylase Arg24Ala mutant · the same entry in another collection · chain C against C, 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 3OPV · PDBe 3OPV · UniProt C9QST6
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