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Crystal structure of T. cruzi histidyl-tRNA synthetase in complex with N-(5-hydroxynaphthalen-2-YL)PROPANAMIDE (chem 1781)
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
- 4YRT
- Type
- protein
- Length
- 414 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidyl-tRNA synthetase
- EC
- 6.1.1.21
- UniProt
- Q4DA54
- Ligands
- HIS, 781, SO4
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 414 | 42% helix, 21% strand | Q4DA54 |
Ligands and binding sites
- HIS · Histidine · ligand · chains A
- 781 · N-(5-hydroxynaphthalen-2-yl)propanamide · ligand · chains A
- SO4 · Sulfate ion · ion · 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.74 | 0.80 | 63 | HIS, 781 |
| 2 | 75 | 0.38 | 0.78 | 15 | empty |
| 3 | 130 | 0.38 | 0.73 | 25 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4YRT · 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 4YRT · PDBe 4YRT · UniProt Q4DA54
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