MolNFT v1 · #28847 · protein
Escherichia COLI purine nucleoside phosphorylase II, the product of the xapa gene
1YQQ · Xanthosine phosphorylase: “Escherichia COLI purine nucleoside phosphorylase II, the product of the xapa gene”. X-ray diffraction, 2 ligands (GUN, PO4), 9 pockets (best druggability 0.86). MolNFT v1 #28847 on GenesisL1: 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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