Research workbench
Structure of E. COLI threonyl-tRNA synthetase complexed with its cognate tRNA
Analyse Structure of E. COLI threonyl-tRNA synthetase complexed with its cognate tRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QF6
- Type
- protein + RNA
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine tRNA; Threonyl-tRNA synthetase
- EC
- 6.1.1.3
- UniProt
- P0A8M3
- Ligands
- AMP, ZN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Threonine tRNA | rna | 76 | — | — |
| A | Threonyl-tRNA synthetase (EC 6.1.1.3) | protein | 641 | 38% helix, 27% strand | P0A8M3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.82 | 0.83 | 97 | ZN, AMP |
| 2 | 320 | 0.58 | 0.78 | 34 | empty |
| 3 | 318 | 0.57 | 0.77 | 31 | empty |
| 4 | 186 | 0.48 | 0.76 | 30 | empty |
| 5 | 144 | 0.40 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 2370 Ų buried · 46 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 7 modified (nucleotide modification).
Compared structures
- 1QF6 · Structure of E. COLI threonyl-tRNA synthetase complexed with its cognate tRNA · the same entry in another collection · chain B against B, TM-score 1.00
- P0A8M3 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase (P0A8M3) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P0A8M3
- Elsewhere: RCSB PDB 1QF6 · PDBe 1QF6 · UniProt P0A8M3
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