MolNFT v1 · #11410 · protein
Structure of the uracil phosphoribosyltransferase GTP complex 2 mutant C128V
1JLR: “Structure of the uracil phosphoribosyltransferase GTP complex 2 mutant C128V”. X-ray diffraction, 2 ligands (GTP, PO4), 11 pockets (best druggability 0.83). MolNFT v1 #11410 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1JLR
- Type
- protein
- Length
- 940 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
- GTP, PO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, C | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 235 | 38% helix, 26% strand | Q26998 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, D, C, B
- PO4 · Phosphate ion · ion · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.83 | 0.84 | 83 | empty |
| 2 | 370 | 0.74 | 0.85 | 37 | empty |
| 3 | 379 | 0.72 | 0.83 | 50 | empty |
| 4 | 466 | 0.71 | 0.81 | 31 | PO4 |
| 5 | 368 | 0.70 | 0.82 | 30 | PO4 |
Interfaces
4 interfaces between chains.
- A–C · 2739 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 2720 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 1163 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1126 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1JLR · Structure of the uracil phosphoribosyltransferase GTP complex 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 1JLR · PDBe 1JLR · UniProt Q26998
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