Research workbench
Crystal structure of human prolyl-tRNA synthetase (prs) in complex with inhibitor
Analyse Crystal structure of human prolyl-tRNA synthetase (prs) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VAD
- Type
- protein
- Length
- 963 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional GLUTAMATE/PROLINE--tRNA ligase
- EC
- 6.1.1.17, 6.1.1.15
- UniProt
- P07814
- Ligands
- 91Y, PRO, ZN
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.17, 6.1.1.15) | protein | 481 | 39% helix, 29% strand | P07814 |
| B | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.17, 6.1.1.15) | protein | 482 | 37% helix, 28% strand | P07814 |
Ligands and binding sites
- 91Y · 3-[(cyclohexanecarbonyl)amino]-N-(2,3-dihydro-1H-inden-2-yl)pyrazine-2-carboxamide · ligand · 2 copies · chains A, B
- PRO · Proline · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.77 | 0.84 | 50 | 91Y, PRO |
| 2 | 573 | 0.76 | 0.83 | 50 | 91Y, PRO |
| 3 | 145 | 0.68 | 0.89 | 29 | empty |
| 4 | 425 | 0.65 | 0.78 | 40 | empty |
| 5 | 302 | 0.63 | 0.80 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2477 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5VAD · Crystal structure of human Prolyl-tRNA synthetase (PRS) in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P07814 · AlphaFold monomer V2.0 prediction for bifunctional GLUTAMATE/PROLINE --tRNA ligase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P07814
- Elsewhere: RCSB PDB 5VAD · PDBe 5VAD · UniProt P07814
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