MolNFT v1 · #154932 · protein
Crystal structure of methylated human leucyl-tRNA synthetase, leu-ams- bound form
6KR7 · Leucine--tRNA ligase, cytoplasmic: “Crystal structure of methylated human leucyl-tRNA synthetase, leu-ams- bound form”. X-ray diffraction, 3 ligands (LEU, LSS, PO4), 9 pockets (best druggability 0.73). MolNFT v1 #154932 on…
- PDB
- 6KR7
- Type
- protein
- Length
- 1,002 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
- LEU, LSS, PO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase, cytoplasmic (EC 6.1.1.4) | protein | 1002 | 47% helix, 15% strand | Q9P2J5 |
Ligands and binding sites
- LEU · Leucine · ligand · chains A
- LSS · 5'-O-(L-leucylsulfamoyl)adenosine · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.73 | 0.82 | 40 | LEU |
| 2 | 679 | 0.72 | 0.79 | 57 | LSS, PO4 |
| 3 | 267 | 0.66 | 0.82 | 32 | empty |
| 4 | 176 | 0.60 | 0.83 | 27 | empty |
| 5 | 119 | 0.52 | 0.81 | 21 | empty |
Compared structures
- 6KR7 · Crystal structure of methylated 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 0.98
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 Q9P2J5
- Elsewhere: RCSB PDB 6KR7 · PDBe 6KR7 · UniProt Q9P2J5
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