Research workbench
Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate hppnp-2
Analyse Crystal structure of H. pylori purine nucleoside phosphorylase from clinical… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MX6
- Type
- protein
- Length
- 1,398 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
- K2JXG0
- Ligands
- HPA, SO4, PO4
- Pockets
- 13 · best druggability 0.71
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 | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 233 | 36% helix, 30% strand | K2JXG0 |
Ligands and binding sites
- HPA · Hypoxanthine · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 9 copies · chains A, D, B, E, C, F
- PO4 · Phosphate ion · ion · chains C, F
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 2 copies · chains A, D, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.71 | 0.77 | 61 | PEG |
| 2 | 386 | 0.68 | 0.81 | 47 | SO4, HPA |
| 3 | 316 | 0.68 | 0.82 | 46 | SO4, HPA |
| 4 | 289 | 0.67 | 0.82 | 45 | SO4, HPA |
| 5 | 369 | 0.66 | 0.80 | 46 | SO4, HPA |
Interfaces
12 interfaces between chains.
- B–D · 1862 Ų buried · 34 hydrogen bonds · protein-protein
- A–F · 1835 Ų buried · 37 hydrogen bonds · protein-protein
- C–F · 1825 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 1788 Ų buried · 37 hydrogen bonds · protein-protein
- B–E · 1693 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5MX6 · Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate… · the same entry in another collection · 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 K2JXG0
- Elsewhere: RCSB PDB 5MX6 · PDBe 5MX6 · UniProt K2JXG0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.