Research workbench
Purine nucleoside PHOSPHORYLASE(DEOD-type) from H. pylori with 2,6- dichloropurine
Analyse Purine nucleoside PHOSPHORYLASE(DEOD-type) from H. pylori with 2,6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OP9
- 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
- 06K, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 29% 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, 29% strand | P56463 |
Ligands and binding sites
- 06K · 2,6-bis(chloranyl)-7H-purine · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 12 copies · chains A, D, B, E, C, F, G, J, H, K, I, L
- IMD · Imidazole · additive · 13 copies · chains A, D, B, E, C, F, G, J, H, K, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.76 | 0.80 | 73 | empty |
| 2 | 901 | 0.76 | 0.79 | 71 | empty |
| 3 | 379 | 0.70 | 0.82 | 54 | 06K, MG, IMD |
| 4 | 362 | 0.69 | 0.82 | 53 | 06K, MG, IMD |
| 5 | 354 | 0.69 | 0.82 | 53 | 06K, MG, IMD |
Interfaces
25 interfaces between chains.
- G–L · 1841 Ų buried · 35 hydrogen bonds · protein-protein
- I–K · 1827 Ų buried · 32 hydrogen bonds · protein-protein
- C–E · 1808 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1805 Ų buried · 31 hydrogen bonds · protein-protein
- H–J · 1802 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (oxidation).
Compared structures
- 7OP9 · Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 2,6-dichloropurine · the same entry in another collection · chain L against L, 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 7OP9 · PDBe 7OP9 · UniProt P56463
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.