MolNFT v1 · #71333 · protein
Crystal structure of purine nucleoside phosphorylase from toxoplasma gondii in complex with immucillin-H
3MB8: “Crystal structure of purine nucleoside phosphorylase from toxoplasma gondii in complex with immucillin-H”. X-ray diffraction, 2 ligands (IMH, PO4), 4 pockets (best druggability 0.74). MolNFT v1 #71333 on GenesisL1: 3D structure…
- PDB
- 3MB8
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- Q2HXR2
- Ligands
- IMH, PO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 248 | 35% helix, 28% strand | Q2HXR2 |
Ligands and binding sites
- IMH · 1,4-dideoxy-4-aza-1-(S)-(9-deazahypoxanthin-9-yl)-D-ribitol · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.74 | 0.89 | 45 | GOL, IMH, PO4 |
| 2 | 229 | 0.73 | 0.88 | 42 | IMH, PO4, GOL |
| 3 | 145 | 0.46 | 0.76 | 16 | empty |
| 4 | 155 | 0.46 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1950 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3MB8 · Crystal structure of purine nucleoside phosphorylase from toxoplasma gondii in complex… · 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 Q2HXR2
- Elsewhere: RCSB PDB 3MB8 · PDBe 3MB8 · UniProt Q2HXR2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.