MolNFT v1 · #111463 · protein
Crystal structure of T. cruzi histidyl-tRNA synthetase in complex with 3-methoxypyridine (chem 443)
4YRM: “Crystal structure of T. cruzi histidyl-tRNA synthetase in complex with 3-methoxypyridine (chem 443)”. X-ray diffraction, 3 ligands (HIS, 282, SO4), 7 pockets (best druggability 0.73). MolNFT v1 #111463 on GenesisL1: 3D structure…
- PDB
- 4YRM
- Type
- protein
- Length
- 826 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, 282, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 412 | 43% helix, 21% strand | Q4DA54 |
| B | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 414 | 43% helix, 21% strand | Q4DA54 |
Ligands and binding sites
- HIS · Histidine · ligand · 2 copies · chains A, B
- 282 · 3-methoxypyridine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.73 | 0.82 | 49 | HIS, 282, SO4 |
| 2 | 469 | 0.73 | 0.83 | 46 | HIS, 282, SO4 |
| 3 | 59 | 0.59 | 0.90 | 18 | empty |
| 4 | 119 | 0.37 | 0.74 | 19 | empty |
| 5 | 79 | 0.37 | 0.77 | 16 | empty |
Compared structures
- 4YRM · Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 3-methoxypyridine… · the same entry in another collection · chain B against B, 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 4YRM · PDBe 4YRM · UniProt Q4DA54
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