MolNFT v1 · #156037 · protein
The crystal structure of human cytoplasmic lrs
6LR6 · Leucine--tRNA ligase, cytoplasmic: “The crystal structure of human cytoplasmic lrs”. X-ray diffraction, 2 ligands (LSS, A2H), 19 pockets (best druggability 0.75). MolNFT v1 #156037 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6LR6
- Type
- protein
- Length
- 2,008 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.4
- UniProt
- Q9P2J5
- Ligands
- LSS, A2H
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase, cytoplasmic (EC 6.1.1.4) | protein | 1003 | 46% helix, 15% strand | Q9P2J5 |
| B | Leucine--tRNA ligase, cytoplasmic (EC 6.1.1.4) | protein | 1005 | 48% helix, 16% strand | Q9P2J5 |
Ligands and binding sites
- LSS · 5'-O-(L-leucylsulfamoyl)adenosine · ligand · 2 copies · chains A, B
- A2H · 4-chloro-3-aminomethyl-7-[ethoxy]-3H-benzo[c][1, 2]oxaborol-1-ol modified adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.75 | 0.82 | 42 | A2H |
| 2 | 443 | 0.74 | 0.83 | 35 | A2H |
| 3 | 701 | 0.71 | 0.78 | 67 | LSS |
| 4 | 651 | 0.70 | 0.78 | 59 | LSS |
| 5 | 160 | 0.67 | 0.87 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 609 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 6LR6 · PDBe 6LR6 · UniProt Q9P2J5
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