Research workbench
Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with L-tryptophanamide
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
- 3KT8
- Type
- protein
- Length
- 1,624 residues
- Chains
- 4
- 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
- LTN, SO4
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase, cytoplasmic (EC 6.1.1.2) | protein | 408 | 48% helix, 12% strand | Q12109 |
| B, C | Tryptophanyl-tRNA synthetase, cytoplasmic (EC 6.1.1.2) | protein | 403 | 49% helix, 12% strand | Q12109 |
| D | Tryptophanyl-tRNA synthetase, cytoplasmic (EC 6.1.1.2) | protein | 410 | 48% helix, 12% strand | Q12109 |
Ligands and binding sites
- LTN · L-tryptophanamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.82 | 0.83 | 108 | LTN, SO4 |
| 2 | 667 | 0.78 | 0.83 | 66 | LTN, SO4 |
| 3 | 360 | 0.78 | 0.88 | 42 | LTN, SO4 |
| 4 | 344 | 0.77 | 0.88 | 41 | LTN, SO4 |
| 5 | 751 | 0.72 | 0.78 | 59 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1569 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1563 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1306 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 408 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 392 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3KT8 · Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q12109 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase, cytoplasmic (Q12109) · a predicted model of the same protein · chain B 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 3KT8 · PDBe 3KT8 · UniProt Q12109
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