Research workbench
Purine nucleoside PHOSPHORYLASE(DEOD-type) from H. pylori with 6- benzylthio-2-chloropurine
Analyse Purine nucleoside PHOSPHORYLASE(DEOD-type) from H. pylori with 6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OOY
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type
- EC
- 2.4.2.1
- UniProt
- P56463
- Ligands
- 05Z, PO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 233 | 35% helix, 29% strand | P56463 |
Ligands and binding sites
- 05Z · 6-benzylthio-2-chloropurine · ligand · chains B
- PO4 · Phosphate ion · ion · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.68 | 0.80 | 44 | GOL |
| 2 | 163 | 0.67 | 0.87 | 34 | TRS, PO4, 05Z, GOL |
| 3 | 70 | 0.33 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1803 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7OOY · Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-benzylthio-2-chloropurine · the same entry in another collection · chain A against A, TM-score 1.00
- P56463 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (P56463) · 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 P56463
- Elsewhere: RCSB PDB 7OOY · PDBe 7OOY · UniProt P56463
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