Research workbench
Crystal structure of histidyl-tRNA synthetase from thermoplasma acidophilum
Analyse Crystal structure of histidyl-tRNA synthetase from thermoplasma acidophilum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WU7
- Type
- protein
- Length
- 844 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidyl-tRNA synthetase
- EC
- 6.1.1.21
- UniProt
- Q9HLX5
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 424 | 40% helix, 21% strand | Q9HLX5 |
| B | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 420 | 38% helix, 21% strand | Q9HLX5 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.83 | 0.84 | 100 | empty |
| 2 | 514 | 0.72 | 0.81 | 52 | empty |
| 3 | 864 | 0.72 | 0.77 | 62 | empty |
| 4 | 152 | 0.49 | 0.78 | 21 | empty |
| 5 | 133 | 0.48 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 4236 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 1WU7 · Crystal structure of histidyl-tRNA synthetase from Thermoplasma acidophilum · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HLX5 · AlphaFold monomer V2.0 prediction for histidine--tRNA ligase (Q9HLX5) · a predicted model of the same protein · chain B 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 Q9HLX5
- Elsewhere: RCSB PDB 1WU7 · PDBe 1WU7 · UniProt Q9HLX5
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