Research workbench
Crystal structure of bacillus caldolyticus uracil phosphoribosyltransferase with bound ump
Analyse Crystal structure of bacillus caldolyticus uracil phosphoribosyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I5E
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil phosphoribosyltransferase
- EC
- 2.4.2.9
- UniProt
- P70881
- Ligands
- U5P
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 208 | 35% helix, 28% strand | P70881 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.59 | 0.78 | 28 | U5P |
| 2 | 296 | 0.58 | 0.77 | 28 | U5P |
| 3 | 63 | 0.53 | 0.87 | 13 | empty |
| 4 | 157 | 0.51 | 0.79 | 17 | empty |
| 5 | 65 | 0.50 | 0.85 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1787 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1I5E · Crystal structure of bacillus caldolyticus uracil phosphoribosyltransferase with bound ump · the same entry in another collection · chain A against A, TM-score 1.00
- P70881 · AlphaFold monomer V2.0 prediction for uracil phosphoribosyltransferase (P70881) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P70881
- Elsewhere: RCSB PDB 1I5E · PDBe 1I5E · UniProt P70881
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