MolNFT v1 · #16345 · protein
Crystal structure of plasmodium falciparum purine nucleoside phosphorylase in complex with immh and sulfate
1NW4 · Uridine phosphorylase, putative: “Crystal structure of plasmodium falciparum purine nucleoside phosphorylase in complex with immh and sulfate”. X-ray diffraction, 2 ligands (IMH, SO4), 16 pockets (best druggability 0.79). MolNFT v1…
- 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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