MolNFT v1 · #139533 · protein
Crystal structure of cryptosporidium parvum prolyl-tRNA synthetase (cpprs) in complex with halofuginone
5XIO · Proline-tRNA synthetase class II aars (ybak RNA binding…: “Crystal structure of cryptosporidium parvum prolyl-tRNA synthetase (cpprs) in complex with halofuginone”. X-ray diffraction, 3 ligands (HFG, ANP, ZN), 9 pockets (best…
- PDB
- 5XIO
- Type
- protein
- Length
- 945 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline-tRNA synthetase class II aars (ybak RNA binding domain plus tRNA synthetase)
- UniProt
- Q5CWN3
- Ligands
- HFG, ANP, ZN
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline-tRNA synthetase class II aars (ybak RNA binding domain plus tRNA synthetase) | protein | 474 | 36% helix, 30% strand | Q5CWN3 |
| B | Proline-tRNA synthetase class II aars (ybak RNA binding domain plus tRNA synthetase) | protein | 471 | 35% helix, 30% strand | Q5CWN3 |
Ligands and binding sites
- 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
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.77 | 0.81 | 56 | HFG, ANP |
| 2 | 733 | 0.77 | 0.81 | 54 | HFG, ANP |
| 3 | 900 | 0.76 | 0.79 | 67 | empty |
| 4 | 640 | 0.67 | 0.76 | 41 | empty |
| 5 | 105 | 0.45 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2425 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5XIO · Crystal Structure of Cryptosporidium parvum Prolyl-tRNA Synthetase (CpPRS) in complex… · 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 Q5CWN3
- Elsewhere: RCSB PDB 5XIO · PDBe 5XIO · UniProt Q5CWN3
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