MolNFT v1 · #139528 · protein
Crystal structure of toxoplasma gondii prolyl-tRNA synthetase (tgprs) in complex with inhibitor 9
5XIJ · Prolyl-tRNA synthetase (prors): “Crystal structure of toxoplasma gondii prolyl-tRNA synthetase (tgprs) in complex with inhibitor 9”. X-ray diffraction, 3 ligands (ANP, 873, MG), 18 pockets (best druggability 0.83). MolNFT v1 #139528…
- PDB
- 5XIJ
- Type
- protein
- Length
- 1,909 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
- Ligands
- ANP, 873, MG
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 482 | 36% helix, 29% strand | S8G8I1 |
| B | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 478 | 36% helix, 29% strand | S8G8I1 |
| C | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 477 | 37% helix, 29% strand | S8G8I1 |
| D | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 472 | 37% helix, 30% strand | S8G8I1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- 873 · 3-[(2R)-2-oxidanyl-3-[(2R,3R)-3-oxidanylpiperidin-2-yl]propyl]quinazolin-4-one · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.83 | 0.84 | 87 | empty |
| 2 | 862 | 0.82 | 0.85 | 77 | empty |
| 3 | 1015 | 0.80 | 0.81 | 93 | empty |
| 4 | 628 | 0.77 | 0.83 | 58 | ANP, MG, 873 |
| 5 | 734 | 0.77 | 0.81 | 58 | ANP, MG, 873 |
Interfaces
4 interfaces between chains.
- C–D · 2692 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2610 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 356 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 354 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XIJ · 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 S8G8I1
- Elsewhere: RCSB PDB 5XIJ · PDBe 5XIJ · UniProt S8G8I1
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