Research workbench
Crystal structure of prolyl-tRNA synthetase (prors, proline--tRNA ligase) from plasmodium falciparum in complex with tcmdc-124506
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
- 4WI1
- Type
- protein
- Length
- 875 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
- 3O6, MG, CL
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline--tRNA ligase (EC 6.1.1.15) | protein | 440 | 39% helix, 28% strand | Q8I5R7 |
| B | Proline--tRNA ligase (EC 6.1.1.15) | protein | 435 | 38% helix, 28% strand | Q8I5R7 |
Ligands and binding sites
- 3O6 · 1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.73 | 0.79 | 54 | EDO |
| 2 | 709 | 0.72 | 0.78 | 61 | EDO |
| 3 | 146 | 0.65 | 0.87 | 27 | empty |
| 4 | 197 | 0.63 | 0.83 | 23 | 3O6 |
| 5 | 194 | 0.63 | 0.83 | 23 | 3O6 |
Interfaces
1 interface between chains.
- A–B · 1824 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4WI1 · 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 0.97
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 4WI1 · PDBe 4WI1 · UniProt Q8I5R7
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