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Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with TrpAMP
Analyse Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KT3
- Type
- protein
- Length
- 1,626 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Saccharomyces cerevisiae
- Molecule
- Tryptophanyl-tRNA synthetase, cytoplasmic
- EC
- 6.1.1.2
- UniProt
- Q12109
- Ligands
- TYM, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.6 · 3 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Tryptophanyl-tRNA synthetase, cytoplasmic (EC 6.1.1.2) | protein | 409 | 49% helix, 11% strand | Q12109 |
| B | Tryptophanyl-tRNA synthetase, cytoplasmic (EC 6.1.1.2) | protein | 405 | 50% helix, 11% strand | Q12109 |
| C | Tryptophanyl-tRNA synthetase, cytoplasmic (EC 6.1.1.2) | protein | 403 | 50% helix, 13% strand | Q12109 |
Ligands and binding sites
- TYM · Tryptophanyl-5'amp · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.80 | 0.81 | 97 | TYM, SO4 |
| 2 | 326 | 0.77 | 0.88 | 39 | TYM, SO4 |
| 3 | 361 | 0.76 | 0.87 | 45 | TYM, SO4 |
| 4 | 399 | 0.75 | 0.85 | 49 | TYM, SO4 |
| 5 | 678 | 0.71 | 0.78 | 61 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1566 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1531 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1520 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 388 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 382 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3KT3 · Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with trpamp · the same entry in another collection · chain A against A, TM-score 1.00
- Q12109 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase, cytoplasmic (Q12109) · a predicted model of the same protein · chain C 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 Q12109
- Elsewhere: RCSB PDB 3KT3 · PDBe 3KT3 · UniProt Q12109
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