Research workbench
Crystal structure of E.COLI purine nucleoside phosphorylase at 0.99 a resolution
Analyse Crystal structure of E.COLI purine nucleoside phosphorylase at 0.99 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RJ2
- Type
- protein
- Length
- 1,422 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
- H0QGF5
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 37% helix, 29% strand | H0QGF5 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, D, C, E, B, 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 | 968 | 0.78 | 0.80 | 68 | empty |
| 2 | 585 | 0.72 | 0.80 | 55 | GOL |
| 3 | 473 | 0.70 | 0.80 | 42 | GOL |
| 4 | 452 | 0.69 | 0.80 | 49 | GOL |
| 5 | 540 | 0.69 | 0.79 | 51 | empty |
Interfaces
12 interfaces between chains.
- A–E · 1792 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 1783 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1746 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1620 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 1577 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4RJ2 · Crystal structure of E.coli purine nucleoside phosphorylase at 0.99 A resolution · 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 H0QGF5
- Elsewhere: RCSB PDB 4RJ2 · PDBe 4RJ2 · UniProt H0QGF5
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