MolNFT v1 · #127457 · protein
Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate hppnp-1
5MX4 · Purine nucleoside phosphorylase deod-type: “Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate hppnp-1”. X-ray diffraction, 2 ligands (HPA, PO4), 13 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 5MX4
- 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, PO4
- Pockets
- 13 · best druggability 0.76
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.76 | 0.80 | 72 | empty |
| 2 | 440 | 0.69 | 0.80 | 47 | empty |
| 3 | 396 | 0.69 | 0.81 | 43 | empty |
| 4 | 396 | 0.68 | 0.81 | 46 | empty |
| 5 | 379 | 0.68 | 0.81 | 51 | empty |
Interfaces
12 interfaces between chains.
- A–F · 1852 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1828 Ų buried · 34 hydrogen bonds · protein-protein
- C–E · 1797 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 1777 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 1666 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5MX4 · 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 5MX4 · PDBe 5MX4 · UniProt K2JXG0
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