Research workbench
Crystal structure of prolyl-tRNA synthetase (prors, proline--tRNA ligase) from plasmodium falciparum in complex with halofuginone and amppnp in space group P212121 at 2.35 a
Analyse Crystal structure of prolyl-tRNA synthetase (prors, proline--tRNA ligase) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q15
- Type
- protein
- Length
- 918 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
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline--tRNA ligase (EC 6.1.1.15) | protein | 460 | 35% helix, 31% strand | Q8I5R7 |
| B | Proline--tRNA ligase (EC 6.1.1.15) | protein | 458 | 35% helix, 31% 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
- EDO · 1,2-ethanediol · additive · 3 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.78 | 0.82 | 74 | empty |
| 2 | 618 | 0.74 | 0.81 | 52 | MG, ANP, HFG |
| 3 | 592 | 0.72 | 0.80 | 56 | MG, ANP, HFG |
| 4 | 608 | 0.71 | 0.79 | 49 | EDO |
| 5 | 106 | 0.40 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2589 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4Q15 · Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium… · 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 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 Q8I5R7
- Elsewhere: RCSB PDB 4Q15 · PDBe 4Q15 · UniProt Q8I5R7
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