Research workbench
Crystal structure of H. pylori purine nucleoside phosphorylase in complex with PO4 and formycin a
Analyse Crystal structure of H. pylori purine nucleoside phosphorylase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F4X
- Type
- protein
- Length
- 1,389 residues
- Chains
- 6
- 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
- FMC, PO4
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 233 | 35% helix, 30% strand | P56463 |
| F | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 224 | 33% helix, 31% strand | P56463 |
Ligands and binding sites
- FMC · (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol · ligand · 6 copies · chains A, D, B, E, C, F
- PO4 · Phosphate ion · ion · 3 copies · chains A, D, C, F, B, E
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, D, B, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.76 | 0.79 | 81 | EDO |
| 2 | 396 | 0.72 | 0.83 | 50 | FMC, PO4 |
| 3 | 437 | 0.72 | 0.82 | 57 | FMC, EDO |
| 4 | 370 | 0.68 | 0.81 | 44 | FMC |
| 5 | 172 | 0.68 | 0.87 | 36 | PO4, FMC |
Interfaces
12 interfaces between chains.
- A–F · 1846 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1846 Ų buried · 33 hydrogen bonds · protein-protein
- B–E · 1813 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 1804 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 1790 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6F4X · Crystal structure of H. pylori purine nucleoside phosphorylase in complex with PO4 and… · the same entry in another collection · chain F against F, 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 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 6F4X · PDBe 6F4X · UniProt P56463
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.