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Crystal structure of the E. COLI pseudouridine synthase trub bound to a T stem-loop RNA
Analyse Crystal structure of the E. COLI pseudouridine synthase trub bound to a T… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K8W
- Type
- protein + RNA
- Length
- 326 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU) P*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'; TRNA…
- EC
- 4.2.1.70
- UniProt
- P60340
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU) P*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3' | rna | 22 | — | — |
| A | TRNA pseudouridine synthase B (EC 4.2.1.70) | protein | 304 | 27% helix, 35% strand | P60340 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.56 | 0.76 | 24 | empty |
| 2 | 57 | 0.31 | 0.76 | 12 | empty |
| 3 | 64 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 1504 Ų buried · 50 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1K8W · Crystal structure of the E. coli pseudouridine synthase TruB bound to a T stem-loop RNA · the same entry in another collection · chain B against B, TM-score 1.00
- P60340 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase B (P60340) · a predicted model of the same protein · chain A 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 P60340
- Elsewhere: RCSB PDB 1K8W · PDBe 1K8W · UniProt P60340
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