MolNFT v1 · #139524 · protein
Crystal structure of prolyl-tRNA synthetase (prs) from toxoplasma gondii
5XIF · Prolyl-tRNA synthetase (prors): “Crystal structure of prolyl-tRNA synthetase (prs) from toxoplasma gondii”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.85). MolNFT v1 #139524 on GenesisL1: 3D structure, binding…
- PDB
- 5XIF
- Type
- protein
- Length
- 941 residues
- Chains
- 2
- 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
- CL
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 473 | 36% helix, 28% strand | S8G8I1 |
| B | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 468 | 37% helix, 29% strand | S8G8I1 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.85 | 0.89 | 77 | CL |
| 2 | 61 | 0.73 | 0.98 | 17 | empty |
| 3 | 362 | 0.69 | 0.82 | 28 | empty |
| 4 | 223 | 0.68 | 0.85 | 27 | empty |
| 5 | 113 | 0.53 | 0.83 | 26 | CL |
Interfaces
1 interface between chains.
- A–B · 2707 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 5XIF · Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Toxoplasma gondii · 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 5XIF · PDBe 5XIF · UniProt S8G8I1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.