Research workbench
Wild-type yeast pseudouridine synthase, PUS1, bound to 5-fluorouracil RNA
Analyse Wild-type yeast pseudouridine synthase, PUS1, bound to 5-fluorouracil RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R9F
- Type
- protein + RNA
- Length
- 392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA pseudouridine synthase 1; RNA (5'- R(*UP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP…
- EC
- 5.4.99.-
- UniProt
- Q12211
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA pseudouridine synthase 1 (EC 5.4.99.-) | protein | 379 | 39% helix, 19% strand | Q12211 |
| B | RNA (5'- R(*UP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP*UP*A)-3') | rna | 13 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.60 | 0.78 | 47 | empty |
| 2 | 115 | 0.58 | 0.85 | 20 | SO4 |
| 3 | 151 | 0.51 | 0.79 | 26 | empty |
| 4 | 60 | 0.47 | 0.84 | 17 | empty |
| 5 | 214 | 0.44 | 0.72 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 591 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7R9F · Wild-type yeast Pseudouridine Synthase, PUS1, bound to 5-Fluorouracil RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q12211 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase 1 (Q12211) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q12211
- Elsewhere: RCSB PDB 7R9F · PDBe 7R9F · UniProt Q12211
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