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The crystal structure of human cytoplasmic LRS
Analyse The crystal structure of human cytoplasmic LRS in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LPF
- Type
- protein
- Length
- 2,008 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.49
- Source
- Homo sapiens
- Molecule
- Leucine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.4
- UniProt
- Q9P2J5
- Ligands
- LSS, VRT
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.49 · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase, cytoplasmic (EC 6.1.1.4) | protein | 1002 | 48% helix, 15% strand | Q9P2J5 |
| B | Leucine--tRNA ligase, cytoplasmic (EC 6.1.1.4) | protein | 1006 | 49% helix, 16% strand | Q9P2J5 |
Ligands and binding sites
- LSS · 5'-O-(L-leucylsulfamoyl)adenosine · ligand · 2 copies · chains A, B
- VRT · 2'-(L-norvalyl)amino-2'-deoxyadenosine · ligand · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.76 | 0.87 | 33 | VRT |
| 2 | 564 | 0.76 | 0.83 | 42 | empty |
| 3 | 649 | 0.71 | 0.79 | 66 | LSS |
| 4 | 642 | 0.70 | 0.78 | 59 | LSS |
| 5 | 236 | 0.67 | 0.84 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 614 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 6LPF · PDBe 6LPF · UniProt Q9P2J5
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