MolNFT v1 · #18839 · protein
Crystal structure of plasmodium falciparum pnp with 5'-methylthio- immucillin-H
1Q1G · Uridine phosphorylase putative: “Crystal structure of plasmodium falciparum pnp with 5'-methylthio- immucillin-H”. X-ray diffraction, 2 ligands (MTI, SO4), 15 pockets (best druggability 0.79). MolNFT v1 #18839 on GenesisL1: 3D…
- PDB
- 1Q1G
- 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
- MTI, SO4
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 34% 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 | 34% helix, 30% strand | Q8I3X4 |
Ligands and binding sites
- MTI · 3,4-dihydroxy-2-[(methylsulfanyl)methyl]-5-(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)pyrrolidinium · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 22 copies · chains A, B, F, C, D, E
- IPA · Isopropyl alcohol · additive · 9 copies · chains A, B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.79 | 0.88 | 55 | SO4, MTI |
| 2 | 369 | 0.79 | 0.88 | 54 | SO4, MTI |
| 3 | 356 | 0.78 | 0.88 | 52 | SO4, MTI |
| 4 | 325 | 0.77 | 0.88 | 46 | SO4, MTI |
| 5 | 363 | 0.77 | 0.87 | 57 | SO4, MTI |
Interfaces
12 interfaces between chains.
- C–D · 2097 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2038 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 2030 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1273 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 1262 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1Q1G · Crystal structure of Plasmodium falciparum PNP with 5'-methylthio-immucillin-H · 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 1Q1G · PDBe 1Q1G · UniProt Q8I3X4
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