Research workbench
Crystal structure of tryptophanyl-tRNA synthetase from campylobacter jejuni
Analyse Crystal structure of tryptophanyl-tRNA synthetase from campylobacter jejuni in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M5W
- Type
- protein
- Length
- 628 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophanyl-tRNA synthetase
- EC
- 6.1.1.2
- UniProt
- Q9PIB4
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 309 | 60% helix, 8% strand | Q9PIB4 |
| B | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 319 | 60% helix, 9% strand | Q9PIB4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.73 | 0.80 | 60 | SO4 |
| 2 | 708 | 0.70 | 0.77 | 66 | GOL |
| 3 | 120 | 0.48 | 0.79 | 21 | empty |
| 4 | 104 | 0.45 | 0.78 | 20 | empty |
| 5 | 67 | 0.36 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1695 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3M5W · Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PIB4 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (Q9PIB4) · 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 Q9PIB4
- Elsewhere: RCSB PDB 3M5W · PDBe 3M5W · UniProt Q9PIB4
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