Research workbench
Crystal structure of tRNA pseudouridine synthase trub and its RNA complex: RNA-protein recognition through a combination of rigid docking and induced fit
Analyse Crystal structure of tRNA pseudouridine synthase trub and its RNA complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R3E
- Type
- protein + RNA
- Length
- 356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*UP*GP*UP*GP*UP*(FHU) P*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'…
- EC
- 4.2.1.70
- UniProt
- Q9WZW0
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-R(*CP*UP*GP*UP*GP*UP*(FHU) P*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3' | rna | 17 | — | — |
| D, E | 5'-R(*CP*UP*GP*UP*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)- 3' | rna | 17 | — | — |
| A | TRNA pseudouridine synthase B (EC 4.2.1.70) | protein | 305 | 21% helix, 36% strand | Q9WZW0 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.72 | 0.76 | 64 | empty |
| 2 | 107 | 0.58 | 0.85 | 21 | empty |
| 3 | 71 | 0.49 | 0.85 | 16 | empty |
| 4 | 52 | 0.28 | 0.75 | 11 | empty |
Interfaces
6 interfaces between chains.
- C–A · 1474 Ų buried · 47 hydrogen bonds · protein-nucleic
- D–E · 743 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- D–A · 311 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–E · 112 Ų buried · 5 hydrogen bonds · nucleic-nucleic
- E–A · 109 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 1R3E · Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9WZW0 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase B (Q9WZW0) · 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 Q9WZW0
- Elsewhere: RCSB PDB 1R3E · PDBe 1R3E · UniProt Q9WZW0
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