Research workbench
Crystal structures of human tryptophanyl-tRNA synthetase in complex with trpamp
Analyse Crystal structures of human tryptophanyl-tRNA synthetase in complex with trpamp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QUJ
- Type
- protein
- Length
- 766 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
- P23381
- Ligands
- TYM, TRP, CL
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 388 | 53% helix, 12% strand | P23381 |
| B | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 378 | 54% helix, 12% strand | P23381 |
Ligands and binding sites
- TYM · Tryptophanyl-5'amp · ligand · chains A
- TRP · Tryptophan · ligand · chains B
- CL · Chloride ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.71 | 0.84 | 39 | TYM |
| 2 | 323 | 0.71 | 0.84 | 42 | TRP |
| 3 | 215 | 0.55 | 0.78 | 28 | CL |
| 4 | 226 | 0.53 | 0.77 | 26 | empty |
| 5 | 191 | 0.51 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1574 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2QUJ · Crystal structures of human tryptophanyl-tRNA synthetase in complex with TrpAMP · the same entry in another collection · chain B against B, TM-score 1.00
- P23381 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase, cytoplasmic (P23381) · 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 P23381
- Elsewhere: RCSB PDB 2QUJ · PDBe 2QUJ · UniProt P23381
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