Research workbench
Crystal structure of prolyl-tRNA synthetase (prors, proline--tRNA ligase) from plasmodium falciparum in complex with glyburide
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
- 5IFU
- Type
- protein
- Length
- 883 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
- GBM, CL
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline--tRNA ligase (EC 6.1.1.15) | protein | 438 | 37% helix, 28% strand | Q8I5R7 |
| B | Proline--tRNA ligase (EC 6.1.1.15) | protein | 445 | 37% helix, 27% strand | Q8I5R7 |
Ligands and binding sites
- GBM · 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl) sulfamoyl]phenyl}ethyl)-2-methoxybenzamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- FMT · Formic acid · additive · 14 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.75 | 0.80 | 63 | FMT, EDO |
| 2 | 699 | 0.72 | 0.78 | 55 | FMT |
| 3 | 198 | 0.61 | 0.81 | 25 | GBM, FMT |
| 4 | 322 | 0.56 | 0.75 | 39 | CL, FMT |
| 5 | 137 | 0.55 | 0.81 | 21 | GBM, FMT |
Interfaces
1 interface between chains.
- A–B · 1739 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5IFU · 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 0.99
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 5IFU · PDBe 5IFU · UniProt Q8I5R7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.