MolNFT v1 · #111456 · protein
Crystal structure of T. cruzi histidyl-tRNA synthetase in complex with 5-bromopyridin-2(1H)-one (chem 148)
4YRF · Histidyl-tRNA synthetase, putative: “Crystal structure of T. cruzi histidyl-tRNA synthetase in complex with 5-bromopyridin-2(1H)-one (chem 148)”. X-ray diffraction, 3 ligands (HIS, 4HS, SO4), 4 pockets (best druggability 0.69).…
- PDB
- 4YRF
- Type
- protein
- Length
- 408 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidyl-tRNA synthetase, putative
- EC
- 6.1.1.21
- UniProt
- Q4DA54
- Ligands
- HIS, 4HS, SO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidyl-tRNA synthetase, putative (EC 6.1.1.21) | protein | 408 | 42% helix, 21% strand | Q4DA54 |
Ligands and binding sites
- HIS · Histidine · ligand · chains A
- 4HS · 5-bromopyridin-2(1H)-one · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.69 | 0.79 | 55 | HIS, 4HS, SO4 |
| 2 | 135 | 0.55 | 0.82 | 24 | empty |
| 3 | 127 | 0.40 | 0.74 | 22 | DMS |
| 4 | 53 | 0.34 | 0.78 | 12 | empty |
Compared structures
- 4YRF · 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 4YRF · PDBe 4YRF · UniProt Q4DA54
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