Research workbench
Crystal structure of plasmodium falciparum purine nucleoside phosphorylase in complex with immh and sulfate
Analyse Crystal structure of plasmodium falciparum purine nucleoside phosphorylase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NW4
- Type
- protein
- Length
- 1,458 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase, putative
- EC
- 2.4.2.1
- UniProt
- Q8I3X4
- Ligands
- IMH, SO4
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Uridine phosphorylase, putative (EC 2.4.2.1) | protein | 243 | 35% helix, 30% strand | Q8I3X4 |
Ligands and binding sites
- IMH · 1,4-dideoxy-4-aza-1-(S)-(9-deazahypoxanthin-9-yl)-D-ribitol · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 19 copies · chains A, B, F, C, D, E
- IPA · Isopropyl alcohol · additive · 15 copies · chains A, B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.79 | 0.88 | 48 | SO4, IMH, IPA |
| 2 | 331 | 0.78 | 0.88 | 50 | SO4, IMH, IPA |
| 3 | 365 | 0.77 | 0.87 | 51 | IPA, SO4, IMH |
| 4 | 353 | 0.77 | 0.87 | 49 | IPA, SO4, IMH |
| 5 | 353 | 0.76 | 0.87 | 47 | IPA, SO4, IMH |
Interfaces
12 interfaces between chains.
- A–B · 2058 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2037 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2025 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1257 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1248 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1NW4 · Crystal Structure of Plasmodium falciparum Purine Nucleoside Phosphorylase in complex… · the same entry in another collection · chain C against C, TM-score 1.00
- Q8I3X4 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (Q8I3X4) · a predicted model of the same protein · 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 Q8I3X4
- Elsewhere: RCSB PDB 1NW4 · PDBe 1NW4 · UniProt Q8I3X4
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