Research workbench
Structure of the apo uracil phosphoribosyltransferase, 2 mutant C128V
Analyse Structure of the apo uracil phosphoribosyltransferase, 2 mutant C128V in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BD3
- Type
- protein
- Length
- 896 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
- PO4
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C, B, A | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 224 | 39% helix, 29% strand | Q26998 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 8 copies · chains D, C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.82 | 0.84 | 84 | empty |
| 2 | 254 | 0.73 | 0.87 | 23 | empty |
| 3 | 424 | 0.72 | 0.82 | 34 | PO4 |
| 4 | 456 | 0.71 | 0.81 | 35 | PO4 |
| 5 | 342 | 0.70 | 0.83 | 30 | PO4 |
Interfaces
4 interfaces between chains.
- D–A · 2182 Ų buried · 28 hydrogen bonds · protein-protein
- C–B · 2119 Ų buried · 31 hydrogen bonds · protein-protein
- C–A · 1194 Ų buried · 16 hydrogen bonds · protein-protein
- D–B · 1149 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1BD3 · Structure of the apo uracil phosphoribosyltransferase, 2 mutant C128V · the same entry in another collection · chain D against D, TM-score 1.00
- Q26998 · AlphaFold monomer V2.0 prediction for uracil phosphoribosyltransferase (Q26998) · a predicted model of the same protein · chain D 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 Q26998
- Elsewhere: RCSB PDB 1BD3 · PDBe 1BD3 · UniProt Q26998
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