Research workbench
Sulfolobus solfataricus uracil phosphoribosyltransferase in complex with uridine 5'-monophosphate (ump)
Analyse Sulfolobus solfataricus uracil phosphoribosyltransferase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XTT
- Type
- protein
- Length
- 846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable uracil phosphoribosyltransferase
- EC
- 2.4.2.9
- UniProt
- Q980Q4
- Ligands
- U5P
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Probable uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 215 | 34% helix, 30% strand | Q980Q4 |
| B, D | Probable uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 208 | 35% helix, 30% strand | Q980Q4 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.87 | 0.88 | 124 | empty |
| 2 | 243 | 0.78 | 0.91 | 32 | U5P |
| 3 | 238 | 0.78 | 0.91 | 35 | U5P |
| 4 | 214 | 0.70 | 0.86 | 26 | U5P |
| 5 | 212 | 0.68 | 0.86 | 28 | U5P |
Interfaces
4 interfaces between chains.
- A–B · 1793 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1786 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1074 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1044 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1XTT · Sulfolobus solfataricus uracil phosphoribosyltransferase in complex with uridine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q980Q4 · AlphaFold monomer V2.0 prediction for uracil phosphoribosyltransferase (Q980Q4) · 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 Q980Q4
- Elsewhere: RCSB PDB 1XTT · PDBe 1XTT · UniProt Q980Q4
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