Research workbench
Crystal structure of toxoplasma gondii prolyl tRNA synthetase (tgprs) in apo form
Analyse Crystal structure of toxoplasma gondii prolyl tRNA synthetase (tgprs) in apo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AA0
- Type
- protein
- Length
- 1,850 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-tRNA synthetase (prors)
- EC
- 6.1.1.15
- UniProt
- S8G8I1
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 470 | 35% helix, 26% strand | S8G8I1 |
| B | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 454 | 38% helix, 25% strand | S8G8I1 |
| C | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 469 | 35% helix, 27% strand | S8G8I1 |
| D | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 457 | 38% helix, 25% strand | S8G8I1 |
Ligands and binding sites
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.85 | 0.90 | 65 | empty |
| 2 | 854 | 0.84 | 0.86 | 100 | GOL |
| 3 | 595 | 0.83 | 0.88 | 70 | empty |
| 4 | 233 | 0.71 | 0.86 | 41 | empty |
| 5 | 382 | 0.70 | 0.82 | 38 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1773 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1746 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 898 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 739 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 682 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6AA0 · Crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in Apo Form · 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 S8G8I1
- Elsewhere: RCSB PDB 6AA0 · PDBe 6AA0 · UniProt S8G8I1
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