Research workbench
Escherichia COLI purine nucleoside phosphorylase II, the product of the xapa gene
Analyse Escherichia COLI purine nucleoside phosphorylase II, the product of the xapa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YQQ
- Type
- protein
- Length
- 819 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthosine phosphorylase
- EC
- 2.4.2.1
- UniProt
- P45563
- Ligands
- GUN, PO4
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Xanthosine phosphorylase (EC 2.4.2.1) | protein | 273 | 33% helix, 25% strand | P45563 |
Ligands and binding sites
- GUN · Guanine · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.86 | 0.95 | 40 | empty |
| 2 | 119 | 0.80 | 0.98 | 27 | GUN, PO4 |
| 3 | 116 | 0.79 | 0.98 | 25 | GUN, PO4 |
| 4 | 108 | 0.79 | 0.98 | 25 | GUN, PO4 |
| 5 | 204 | 0.44 | 0.73 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–C · 998 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 997 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 964 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1YQQ · Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene · the same entry in another collection · chain A against A, TM-score 1.00
- P45563 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase 2 (P45563) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P45563
- Elsewhere: RCSB PDB 1YQQ · PDBe 1YQQ · UniProt P45563
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