MolNFT v1 · #177849 · protein
Co-crystal structure of toxoplasma gondii prolyl tRNA synthetase (tgprs) in complex with JE6 and L-pro
7EVV · Prolyl-tRNA synthetase (prors): “Co-crystal structure of toxoplasma gondii prolyl tRNA synthetase (tgprs) in complex with JE6 and L-pro”. X-ray diffraction, 3 ligands (JE6, PRO, CL), 5 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 7EVV
- Type
- protein
- Length
- 489 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-tRNA synthetase (prors)
- UniProt
- A0A7J6JUK2
- Ligands
- JE6, PRO, CL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 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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