Research workbench
Plasmodium falciparum tyrosyl-tRNA synthetase, S234C mutant, in complex with ML901-tyr
Analyse Plasmodium falciparum tyrosyl-tRNA synthetase, S234C mutant, 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
- 7ROT
- Type
- protein
- Length
- 700 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
- 66I, MG, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 348 | 57% helix, 9% strand | Q8IAR7 |
| B | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 352 | 57% helix, 11% strand | Q8IAR7 |
Ligands and binding sites
- 66I · {(2R,3S,4R,5R)-5-[4-amino-3-(difluoromethoxy)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-dihydroxyoxolan-2-yl}methyl [(2S)-2-amino-3-(4-hydroxyphenyl) propanoyl]sulfamate (non-preferred name) · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 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 | 434 | 0.67 | 0.79 | 44 | 66I |
| 2 | 467 | 0.67 | 0.79 | 49 | 66I |
| 3 | 201 | 0.48 | 0.75 | 26 | empty |
| 4 | 139 | 0.45 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1370 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7ROT · Plasmodium falciparum tyrosyl-tRNA synthetase, S234C mutant, in complex with ML901-Tyr · 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 7ROT · PDBe 7ROT · UniProt Q8IAR7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.