MolNFT v1 · #61943 · protein
Crystal structure of schistosoma mansoni purine nucleoside phosphorylase complexed with a novel monocyclic inhibitor
3E0Q · Purine-nucleoside phosphorylase: “Crystal structure of schistosoma mansoni purine nucleoside phosphorylase complexed with a novel monocyclic…”. X-ray diffraction, 1 ligand (JFD), 5 pockets (best druggability 0.77). MolNFT v1 #61943…
- PDB
- 3E0Q
- Type
- protein
- Length
- 831 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine-nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- Q9BMI9
- Ligands
- JFD
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 280 | 36% helix, 23% strand | Q9BMI9 |
| B | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 266 | 34% helix, 25% strand | Q9BMI9 |
| C | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 285 | 35% helix, 25% strand | Q9BMI9 |
Ligands and binding sites
- JFD · 6-amino-5-bromo-1,2,3,4-tetrahydropyrimidine-2,4-dione · ligand · 3 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.77 | 0.99 | 21 | DMS |
| 2 | 419 | 0.66 | 0.79 | 45 | JFD |
| 3 | 349 | 0.63 | 0.79 | 39 | JFD |
| 4 | 208 | 0.50 | 0.76 | 39 | JFD |
| 5 | 200 | 0.43 | 0.73 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1307 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1269 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1136 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3E0Q · Crystal structure of Schistosoma mansoni purine nucleoside phosphorylase complexed with a… · 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 Q9BMI9
- Elsewhere: RCSB PDB 3E0Q · PDBe 3E0Q · UniProt Q9BMI9
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