MolNFT v1 · #184400 · protein
Purine nucleoside PHOSPHORYLASE(DEOD-type) from H. pylori with 6- benzyloxo-2-chloropurine
7OOZ · Purine nucleoside phosphorylase deod-type: “Purine nucleoside PHOSPHORYLASE(DEOD-type) from H. pylori with 6- benzyloxo-2-chloropurine”. X-ray diffraction, 3 ligands (05Q, MG, PO4), 4 pockets (best druggability 0.66). MolNFT v1…
- PDB
- 7OOZ
- 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
- 05Q, MG, PO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 36% 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 | 36% helix, 29% strand | P56463 |
Ligands and binding sites
- 05Q · 6-benzyloxo-2-chloropurine · ligand · chains B
- MG · Magnesium ion · metal · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
- GOL · Glycerol · additive · 18 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.66 | 0.84 | 37 | 05Q, TRS, PO4, GOL |
| 2 | 362 | 0.65 | 0.80 | 46 | GOL, MG |
| 3 | 105 | 0.37 | 0.75 | 23 | empty |
| 4 | 70 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1815 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7OOZ · Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-benzyloxo-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 7OOZ · PDBe 7OOZ · UniProt P56463
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