Research workbench
Crystal structure of prolyl-tRNA synthetase from cryptosporidium parvum complexed with L-proline and AMP
Analyse Crystal structure of prolyl-tRNA synthetase from cryptosporidium parvum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F9Y
- Type
- protein
- Length
- 955 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoacyl-tRNA synthetase
- UniProt
- Q7YZ69
- Ligands
- PRO, AMP, ZN, PO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoacyl-tRNA synthetase | protein | 488 | 34% helix, 28% strand | Q7YZ69 |
| B | Aminoacyl-tRNA synthetase | protein | 467 | 36% helix, 29% strand | Q7YZ69 |
Ligands and binding sites
- PRO · Proline · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains 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 | 929 | 0.74 | 0.78 | 73 | empty |
| 2 | 456 | 0.65 | 0.78 | 56 | PRO, AMP |
| 3 | 414 | 0.65 | 0.78 | 54 | PRO, AMP, PO4 |
| 4 | 516 | 0.64 | 0.76 | 35 | empty |
| 5 | 88 | 0.57 | 0.87 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2213 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5F9Y · Crystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium parvum complexed with… · the same entry in another collection · chain B against B, 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 5F9Y · PDBe 5F9Y · UniProt Q7YZ69
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