MolNFT v1 · #118700 · protein
Crystal structure of prolyl-tRNA synthetase from cryptosporidium parvum complexed with halofuginone and amppnp
5F9Z · Aminoacyl-tRNA synthetase: “Crystal structure of prolyl-tRNA synthetase from cryptosporidium parvum complexed with halofuginone and amppnp”. X-ray diffraction, 4 ligands (ANP, HFG, MG), 9 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 5F9Z
- Type
- protein
- Length
- 981 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoacyl-tRNA synthetase
- UniProt
- Q7YZ69
- Ligands
- ANP, HFG, MG, ZN
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoacyl-tRNA synthetase | protein | 493 | 35% helix, 28% strand | Q7YZ69 |
| B | Aminoacyl-tRNA synthetase | protein | 488 | 34% helix, 29% strand | Q7YZ69 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- HFG · 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.76 | 0.78 | 73 | GOL |
| 2 | 625 | 0.75 | 0.82 | 56 | MG, ANP, HFG |
| 3 | 591 | 0.71 | 0.79 | 53 | MG, ANP, HFG |
| 4 | 621 | 0.66 | 0.75 | 45 | empty |
| 5 | 101 | 0.59 | 0.86 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2376 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5F9Z · Crystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium parvum complexed 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 Q7YZ69
- Elsewhere: RCSB PDB 5F9Z · PDBe 5F9Z · UniProt Q7YZ69
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.