MolNFT v1 · #154655 · protein
Crystal structure of human leucyl-tRNA synthetase, leu-ams-bound form
6KIE · Leucine--tRNA ligase, cytoplasmic: “Crystal structure of human leucyl-tRNA synthetase, leu-ams-bound form”. X-ray diffraction, 3 ligands (LSS, LEU, PO4), 10 pockets (best druggability 0.77). MolNFT v1 #154655 on GenesisL1: 3D…
- PDB
- 6KIE
- Type
- protein
- Length
- 1,004 residues
- Chains
- 1
- 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, LEU, PO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase, cytoplasmic (EC 6.1.1.4) | protein | 1004 | 45% helix, 14% strand | Q9P2J5 |
Ligands and binding sites
- LSS · 5'-O-(L-leucylsulfamoyl)adenosine · ligand · chains A
- LEU · Leucine · ligand · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.77 | 0.93 | 21 | empty |
| 2 | 896 | 0.75 | 0.79 | 71 | PO4, LSS |
| 3 | 323 | 0.69 | 0.83 | 33 | LEU |
| 4 | 295 | 0.66 | 0.82 | 36 | empty |
| 5 | 104 | 0.62 | 0.88 | 21 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6KIE · Crystal structure of human leucyl-tRNA synthetase, Leu-AMS-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 0.97
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 6KIE · PDBe 6KIE · UniProt Q9P2J5
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