Research workbench
Crystal structure of human leucyl-tRNA synthetase, Leucine-bound form
Analyse Crystal structure of human leucyl-tRNA synthetase, Leucine-bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KQY
- Type
- protein
- Length
- 1,002 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Homo sapiens
- Molecule
- Leucine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.4
- UniProt
- Q9P2J5
- Ligands
- LEU, PO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · resolution 3.3 · 1 distinct chain · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase, cytoplasmic (EC 6.1.1.4) | protein | 1002 | 41% helix, 13% strand | Q9P2J5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.80 | 0.97 | 22 | empty |
| 2 | 812 | 0.75 | 0.79 | 69 | LEU, PO4 |
| 3 | 88 | 0.75 | 0.96 | 22 | empty |
| 4 | 443 | 0.73 | 0.83 | 55 | empty |
| 5 | 135 | 0.63 | 0.86 | 25 | empty |
Compared structures
- 6KQY · Crystal structure of human leucyl-tRNA synthetase, leucine-bound form · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P2J5 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase, cytoplasmic (Q9P2J5) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9P2J5
- Elsewhere: RCSB PDB 6KQY · PDBe 6KQY · UniProt Q9P2J5
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