Research workbench
Crystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic archaeon, aeropyrum pernix K1 complex with tryptophan
Analyse Crystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A05
- Type
- protein
- Length
- 367 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophanyl-tRNA synthetase
- EC
- 6.1.1.2
- UniProt
- Q9Y924
- Ligands
- TRP, SF4, CD
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 367 | 56% helix, 10% strand | Q9Y924 |
Ligands and binding sites
- TRP · Tryptophan · ligand · chains A
- SF4 · Iron/sulfur cluster · ligand · chains A
- CD · Cadmium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.70 | 0.80 | 47 | TRP, CD |
| 2 | 152 | 0.43 | 0.74 | 23 | empty |
| 3 | 82 | 0.39 | 0.78 | 25 | CD |
| 4 | 63 | 0.31 | 0.75 | 16 | empty |
Compared structures
- 3A05 · Crystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic archaeon… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y924 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (Q9Y924) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9Y924
- Elsewhere: RCSB PDB 3A05 · PDBe 3A05 · UniProt Q9Y924
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