Research workbench
Plasmodium falciparum tyrosyl-tRNA synthetase in complex with tyrosine-AMP
Analyse Plasmodium falciparum tyrosyl-tRNA synthetase in complex with tyrosine-AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ROR
- Type
- protein
- Length
- 718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine--tRNA ligase
- EC
- 6.1.1.1
- UniProt
- Q8IAR7
- Ligands
- 69X, MG, CL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 356 | 56% helix, 11% strand | Q8IAR7 |
| B | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 362 | 57% helix, 11% strand | Q8IAR7 |
Ligands and binding sites
- 69X · 5'-O-[(S)-{[(2S)-2-amino-3-(4-hydroxyphenyl) propanoyl]oxy}(hydroxy)phosphoryl]adenosine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A
- MLI · Malonate ion · additive · 4 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 | 326 | 0.78 | 0.89 | 40 | 69X, MLI |
| 2 | 332 | 0.77 | 0.88 | 45 | 69X, MLI |
| 3 | 204 | 0.48 | 0.75 | 32 | empty |
| 4 | 150 | 0.46 | 0.76 | 26 | empty |
| 5 | 94 | 0.38 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1363 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7ROR · Plasmodium falciparum tyrosyl-tRNA synthetase in complex with tyrosine-AMP · 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 Q8IAR7
- Elsewhere: RCSB PDB 7ROR · PDBe 7ROR · UniProt Q8IAR7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.