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Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with (6-bromopyridin-2-yl)methanol (Chem 149)
Analyse Crystal structure of T. cruzi Histidyl-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
- 4YRG
- Type
- protein
- Length
- 403 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Trypanosoma cruzi (strain CL Brener)
- Molecule
- Histidyl-tRNA synthetase
- EC
- 6.1.1.21
- UniProt
- Q4DA54
- Ligands
- HIS, 4HU, SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.15 · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 403 | 42% helix, 22% strand | Q4DA54 |
Ligands and binding sites
- HIS · Histidine · ligand · chains A
- 4HU · (6-bromopyridin-2-yl)methanol · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 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 | 526 | 0.72 | 0.81 | 45 | HIS, 4HU, SO4 |
| 2 | 109 | 0.46 | 0.79 | 24 | empty |
| 3 | 80 | 0.38 | 0.77 | 15 | empty |
| 4 | 116 | 0.37 | 0.74 | 21 | DMS |
Compared structures
- 4YRG · Crystal structure of T. cruzi histidyl-tRNA synthetase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q4DA54
- Elsewhere: RCSB PDB 4YRG · PDBe 4YRG · UniProt Q4DA54
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