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Arsenolytic structure of plasmodium falciparum purine nucleoside phosphorylase with hypoxanthine, ribose and arsenate ion
Analyse Arsenolytic structure of plasmodium falciparum purine nucleoside phosphorylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ENZ
- Type
- protein
- Length
- 1,465 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- Q8I3X4
- Ligands
- HPA, R1X, ART, NA
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 244 | 36% helix, 30% strand | Q8I3X4 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 245 | 37% helix, 30% strand | Q8I3X4 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 246 | 35% helix, 29% strand | Q8I3X4 |
| E, F | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 243 | 34% helix, 30% strand | Q8I3X4 |
Ligands and binding sites
- HPA · Hypoxanthine · ligand · 6 copies · chains A, B, C, D, E, F
- R1X · 1,4-anhydro-D-ribitol · ligand · 6 copies · chains A, B, C, E, D, F
- ART · Arsenate · ligand · 6 copies · chains A, B, C, E, D, F
- NA · Sodium ion · metal · 5 copies · chains A, B, D, C, E, F
- FMT · Formic acid · additive · 24 copies · chains A, B, C, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.75 | 0.88 | 49 | HPA, R1X, ART |
| 2 | 240 | 0.73 | 0.88 | 38 | HPA, R1X, ART |
| 3 | 258 | 0.73 | 0.87 | 40 | HPA, R1X, ART, FMT |
| 4 | 1147 | 0.72 | 0.76 | 129 | HPA, R1X, ART, FMT |
| 5 | 248 | 0.72 | 0.87 | 41 | HPA, R1X, ART |
Interfaces
12 interfaces between chains.
- A–B · 2116 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 2088 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 2081 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1265 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1260 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3ENZ · Arsenolytic structure of Plasmodium falciparum purine nucleoside phosphorylase with… · the same entry in another collection · chain F against F, TM-score 1.00
- Q8I3X4 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (Q8I3X4) · a predicted model of the same protein · chain E 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 Q8I3X4
- Elsewhere: RCSB PDB 3ENZ · PDBe 3ENZ · UniProt Q8I3X4
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