Research workbench
Purine nucleoside PHOSPHORYLASE(DEOD-type) from H. pylori with 6- benzylthiopurine
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
- 7OPA
- Type
- protein
- Length
- 2,796 residues
- Chains
- 12
- 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
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 233 | 36% helix, 30% strand | P56463 |
Ligands and binding sites
- 05Z · 6-benzylthio-2-chloropurine · ligand · 2 copies · chains C, H
- PO4 · Phosphate ion · ion · 2 copies · chains C, F, H, K
- GOL · Glycerol · additive · 20 copies · chains A, D, B, E, C, F, H, J, K, G, I
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains C, F, H, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.77 | 0.81 | 75 | empty |
| 2 | 817 | 0.76 | 0.80 | 75 | empty |
| 3 | 324 | 0.71 | 0.84 | 54 | GOL |
| 4 | 615 | 0.70 | 0.79 | 49 | GOL |
| 5 | 494 | 0.69 | 0.79 | 52 | GOL |
Interfaces
27 interfaces between chains.
- G–L · 1876 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1857 Ų buried · 34 hydrogen bonds · protein-protein
- A–F · 1834 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 1833 Ų buried · 5 hydrogen bonds · protein-protein
- H–K · 1816 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7OPA · Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-benzylthiopurine · the same entry in another collection · chain H against H, TM-score 1.00
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 7OPA · PDBe 7OPA · UniProt P56463
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