Research workbench
Crystal structure of E.coli purine nucleoside phosphorylase with acycloguanosine
Analyse Crystal structure of E.coli purine nucleoside phosphorylase with acycloguanosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I3C
- Type
- protein
- Length
- 711 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.32
- Source
- Escherichia coli O139:H28 (strain E24377A / ETEC)
- Molecule
- Purine nucleoside phosphorylase DeoD-type
- EC
- 2.4.2.1
- UniProt
- A7ZVS7
- Ligands
- AC2, SO4
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · resolution 2.32 · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Purine nucleoside phosphorylase DeoD-type (EC 2.4.2.1) | protein | 237 | 35% helix, 27% strand | A7ZVS7 |
Ligands and binding sites
- AC2 · 9-hyroxyethoxymethylguanine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.59 | 0.79 | 44 | AC2, SO4 |
| 2 | 270 | 0.57 | 0.78 | 41 | AC2, SO4 |
| 3 | 275 | 0.56 | 0.76 | 47 | AC2, SO4 |
| 4 | 115 | 0.36 | 0.74 | 18 | empty |
| 5 | 67 | 0.33 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 133 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 129 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 125 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5I3C · Crystal structure of E.COLI purine nucleoside phosphorylase with acycloguanosine · the same entry in another collection · chain A against A, TM-score 1.00
- A7ZVS7 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (A7ZVS7) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 A7ZVS7
- Elsewhere: RCSB PDB 5I3C · PDBe 5I3C · UniProt A7ZVS7
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