MolNFT v1 · #142616 · protein
Crystal structure of toxoplasma gondii prolyl tRNA synthetase (tgprs) in apo form
6AA0 · Prolyl-tRNA synthetase (prors): “Crystal structure of toxoplasma gondii prolyl tRNA synthetase (tgprs) in apo form”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #142616 on GenesisL1: 3D structure, binding sites…
- 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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