MolNFT v1 · #145211 · protein
Crystal structure of human lysyl-tRNA synthetase complexed with L- lysylsulfamoyl adenosine
6CHD · Lysine--tRNA ligase: “Crystal structure of human lysyl-tRNA synthetase complexed with L- lysylsulfamoyl adenosine”. X-ray diffraction, 2 ligands (KAA, SO4), 10 pockets (best druggability 0.84). MolNFT v1 #145211 on GenesisL1: 3D…
- PDB
- 6CHD
- Type
- protein
- Length
- 1,008 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase
- EC
- 2.7.7.-, 6.1.1.6
- UniProt
- Q15046
- Ligands
- KAA, SO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 2.7.7.-, 6.1.1.6) | protein | 506 | 35% helix, 25% strand | Q15046 |
| B | Lysine--tRNA ligase (EC 2.7.7.-, 6.1.1.6) | protein | 502 | 36% helix, 25% strand | Q15046 |
Ligands and binding sites
- KAA · 5'-O-[(L-lysylamino)sulfonyl]adenosine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- GOL · Glycerol · additive · chains B
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 | 428 | 0.84 | 0.92 | 87 | empty |
| 2 | 763 | 0.79 | 0.83 | 78 | KAA |
| 3 | 724 | 0.79 | 0.83 | 75 | KAA, SO4 |
| 4 | 277 | 0.75 | 0.88 | 37 | empty |
| 5 | 134 | 0.66 | 0.88 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 4398 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
- 6CHD · Crystal Structure of Human Lysyl-tRNA Synthetase complexed with L-Lysylsulfamoyl Adenosine · the same entry in another collection · chain A against A, TM-score 1.00
- Q15046 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase (Q15046) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q15046
- Elsewhere: RCSB PDB 6CHD · PDBe 6CHD · UniProt Q15046
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