Research workbench
Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with JE6 and L-pro
Analyse Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EVV
- Type
- protein
- Length
- 489 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.704
- Source
- Toxoplasma gondii
- Molecule
- Prolyl-tRNA synthetase (ProRS)
- UniProt
- A0A7J6JUK2
- Ligands
- JE6, PRO, CL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.704 · 1 distinct chain · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-tRNA synthetase (ProRS) | protein | 489 | 36% helix, 28% strand | A0A7J6JUK2 |
Ligands and binding sites
- JE6 · ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide · ligand · chains A
- PRO · Proline · ligand · chains A
- CL · Chloride ion · ion
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.73 | 0.79 | 67 | JE6, PRO |
| 2 | 301 | 0.54 | 0.75 | 38 | empty |
| 3 | 105 | 0.54 | 0.83 | 16 | MPD |
| 4 | 106 | 0.38 | 0.74 | 18 | empty |
| 5 | 59 | 0.30 | 0.75 | 16 | empty |
Compared structures
- 7EVV · Co-crystal structure of toxoplasma gondii prolyl tRNA synthetase (tgprs) 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 A0A7J6JUK2
- Elsewhere: RCSB PDB 7EVV · PDBe 7EVV · UniProt A0A7J6JUK2
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