MolNFT v1 · #111004 · protein
Crystal structure of prolyl-tRNA synthetase (prs) from plasmodium falciparum in complex with halofuginone and amppnp
4YDQ · Proline--tRNA ligase: “Crystal structure of prolyl-tRNA synthetase (prs) from plasmodium falciparum in complex with halofuginone and…”. X-ray diffraction, 3 ligands (ANP, HFG, MG), 8 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 4YDQ
- Type
- protein
- Length
- 964 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline--tRNA ligase
- EC
- 6.1.1.15
- UniProt
- Q8I5R7
- Ligands
- ANP, HFG, MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline--tRNA ligase (EC 6.1.1.15) | protein | 486 | 36% helix, 28% strand | Q8I5R7 |
| B | Proline--tRNA ligase (EC 6.1.1.15) | protein | 478 | 36% helix, 29% strand | Q8I5R7 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.80 | 0.84 | 64 | ANP, HFG, MG |
| 2 | 835 | 0.76 | 0.80 | 75 | ANP, HFG, MG |
| 3 | 705 | 0.73 | 0.79 | 54 | empty |
| 4 | 294 | 0.70 | 0.84 | 37 | empty |
| 5 | 638 | 0.70 | 0.78 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 2615 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4YDQ · Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8I5R7 · AlphaFold monomer V2.0 prediction for proline--tRNA ligase (Q8I5R7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8I5R7
- Elsewhere: RCSB PDB 4YDQ · PDBe 4YDQ · UniProt Q8I5R7
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