MolNFT v1 · #69522 · protein
Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase
3KT0 · Tryptophanyl-tRNA synthetase, cytoplasmic: “Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase”. X-ray diffraction, 1 ligand (EMN), 3 pockets (best druggability 0.69). MolNFT v1 #69522 on GenesisL1: 3D structure…
- PDB
- 3KT0
- Type
- protein
- Length
- 373 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophanyl-tRNA synthetase, cytoplasmic
- EC
- 6.1.1.2
- UniProt
- Q12109
- Ligands
- EMN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase, cytoplasmic (EC 6.1.1.2) | protein | 373 | 53% helix, 10% strand | Q12109 |
Ligands and binding sites
- EMN · (2S)-1-{[(2S)-3-(2-methoxyethoxy)-2-methylpropyl]oxy}propan-2-amine · ligand · chains 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 | 663 | 0.69 | 0.77 | 66 | EMN |
| 2 | 84 | 0.42 | 0.79 | 19 | empty |
| 3 | 129 | 0.39 | 0.74 | 18 | empty |
Compared structures
- 3KT0 · Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase · 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 A against A, TM-score 0.98
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 3KT0 · PDBe 3KT0 · UniProt Q12109
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