Research workbench
Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA
Analyse Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NRE
- Type
- protein + RNA
- Length
- 315 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4
- Source
- Escherichia coli K12; SYNTHETIC CONSTRUCT
- Molecule
- leucyl tRNA; tRNA pseudouridine synthase A
- EC
- 5.4.99.12
- UniProt
- P07649
- Ligands
- K
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · resolution 4 · 2 distinct chains · 21% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | leucyl tRNA | rna | 56 | — | — |
| A | tRNA pseudouridine synthase A (EC 5.4.99.12) | protein | 259 | 21% helix, 20% strand | P07649 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.68 | 0.77 | 41 | empty |
| 2 | 541 | 0.61 | 0.75 | 50 | empty |
| 3 | 342 | 0.55 | 0.76 | 23 | empty |
| 4 | 79 | 0.37 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- F–A · 506 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 2NRE · Crystal structure of pseudoudirinde synthase trua in complex with leucyl tRNA · the same entry in another collection · chain A against A, TM-score 1.00
- P07649 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase a (P07649) · 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 P07649
- Elsewhere: RCSB PDB 2NRE · PDBe 2NRE · UniProt P07649
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.