MolNFT v1 · #148400 · protein
Crystal structure of H. pylori purine nucleoside phosphorylase
6F5I · Purine nucleoside phosphorylase deod-type: “Crystal structure of H. pylori purine nucleoside phosphorylase”. X-ray diffraction, 14 pockets (best druggability 0.74). MolNFT v1 #148400 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6F5I
- 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
- P56463
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 29% 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 | 34% helix, 29% strand | P56463 |
Ligands and binding sites
- MOH · Methanol · additive · 4 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.74 | 0.79 | 79 | empty |
| 2 | 58 | 0.72 | 0.98 | 21 | empty |
| 3 | 202 | 0.69 | 0.86 | 41 | MOH |
| 4 | 331 | 0.69 | 0.82 | 43 | empty |
| 5 | 382 | 0.69 | 0.81 | 55 | empty |
Interfaces
12 interfaces between chains.
- B–E · 1829 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1826 Ų buried · 30 hydrogen bonds · protein-protein
- C–E · 1820 Ų buried · 34 hydrogen bonds · protein-protein
- A–F · 1817 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1792 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6F5I · Crystal structure of H. pylori purine nucleoside phosphorylase · 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 E against A, TM-score 0.99
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 6F5I · PDBe 6F5I · UniProt P56463
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