MolNFT v1 · #111461 · protein
Crystal structure of T. cruzi histidyl-tRNA synthetase in complex with (4-CHLOROPHENYL)METHANOL (chem 260)
4YRK: “Crystal structure of T. cruzi histidyl-tRNA synthetase in complex with (4-CHLOROPHENYL)METHANOL (chem 260)”. X-ray diffraction, 3 ligands (HIS, 4JL, SO4), 6 pockets (best druggability 0.75). MolNFT v1 #111461 on GenesisL1: 3D…
- PDB
- 4YRK
- Type
- protein
- Length
- 822 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
- Q4DA54
- Ligands
- HIS, 4JL, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 411 | 42% helix, 21% strand | Q4DA54 |
| B | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 411 | 43% helix, 21% strand | Q4DA54 |
Ligands and binding sites
- HIS · Histidine · ligand · 2 copies · chains A, B
- 4JL · (4-chlorophenyl)methanol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.75 | 0.84 | 46 | HIS, 4JL, SO4 |
| 2 | 555 | 0.74 | 0.82 | 59 | HIS, 4JL, SO4 |
| 3 | 131 | 0.40 | 0.75 | 27 | DMS |
| 4 | 123 | 0.39 | 0.74 | 23 | DMS |
| 5 | 71 | 0.34 | 0.75 | 14 | empty |
Compared structures
- 4YRK · 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 4YRK · PDBe 4YRK · UniProt Q4DA54
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