MolNFT v1 · #11411 · protein
Structure of the uracil phosphoribosyltransferase URACIL/CPR 2 mutant C128V
1JLS: “Structure of the uracil phosphoribosyltransferase URACIL/CPR 2 mutant C128V”. X-ray diffraction, 4 ligands (URA, PRP, MG), 15 pockets (best druggability 0.83). MolNFT v1 #11411 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1JLS
- Type
- protein
- Length
- 885 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil phosphoribosyltransferase
- EC
- 2.4.2.9
- UniProt
- Q26998
- Ligands
- URA, PRP, MG, PO4
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 224 | 38% helix, 27% strand | Q26998 |
| A, D | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 219 | 37% helix, 27% strand | Q26998 |
| C | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 223 | 38% helix, 27% strand | Q26998 |
Ligands and binding sites
- URA · Uracil · ligand · 4 copies · chains B, A, D, C
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · chains B, A
- MG · Magnesium ion · metal · chains B
- PO4 · Phosphate ion · ion · 9 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.83 | 0.84 | 80 | empty |
| 2 | 218 | 0.74 | 0.89 | 21 | empty |
| 3 | 489 | 0.72 | 0.82 | 31 | PO4, URA |
| 4 | 402 | 0.71 | 0.82 | 33 | MG, URA, PRP |
| 5 | 230 | 0.70 | 0.85 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2171 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 2162 Ų buried · 31 hydrogen bonds · protein-protein
- B–A · 1145 Ų buried · 12 hydrogen bonds · protein-protein
- D–C · 1124 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 43 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1JLS · Structure of the uracil phosphoribosyltransferase URACIL/CPR 2 mutant C128V · the same entry in another collection · chain A against A, TM-score 1.00
- Q26998 · AlphaFold monomer V2.0 prediction for uracil phosphoribosyltransferase (Q26998) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q26998
- Elsewhere: RCSB PDB 1JLS · PDBe 1JLS · UniProt Q26998
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