Research workbench
Crystal structure of prolyl-tRNA synthetase (prors, proline-tRNA ligase) from plasmodium falciparum in complex with MAT345 and L- proline
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
- 7QB7
- Type
- protein
- Length
- 486 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline--tRNA ligase
- EC
- 6.1.1.15
- UniProt
- Q8I5R7
- Ligands
- PRO, 9X2
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 28% 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 |
Ligands and binding sites
- PRO · Proline · ligand · chains A
- 9X2 · ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-[[4-[[[(2~{S})-pyrrolidin-2-yl]carbonylamino]methyl]piperidin-1-yl]carbonylamino]pyrazine-2-carboxamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 13 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.75 | 0.82 | 52 | PRO, 9X2 |
| 2 | 99 | 0.52 | 0.83 | 22 | empty |
| 3 | 185 | 0.50 | 0.77 | 32 | empty |
| 4 | 102 | 0.48 | 0.80 | 15 | EDO |
| 5 | 53 | 0.46 | 0.84 | 13 | EDO |
Compared structures
- 7QB7 · 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 7QB7 · PDBe 7QB7 · UniProt Q8I5R7
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