Research workbench
Lysyl-tRNA synthetase from bacillus stearothermophilus complexed with diadenosine tetraphosphate (AP4A)
Analyse Lysyl-tRNA synthetase from bacillus stearothermophilus complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A74
- Type
- protein
- Length
- 1,936 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysyl-tRNA synthetase
- EC
- 6.1.1.6
- UniProt
- Q9RHV9
- Ligands
- B4P, LYN, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lysyl-tRNA synthetase (EC 6.1.1.6) | protein | 484 | 37% helix, 27% strand | Q9RHV9 |
Ligands and binding sites
- B4P · Bis(adenosine)-5'-tetraphosphate · ligand · 4 copies · chains A, B, C, D
- LYN · 2,6-diamino-hexanoic acid amide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.84 | 0.96 | 53 | empty |
| 2 | 165 | 0.82 | 0.97 | 36 | empty |
| 3 | 583 | 0.77 | 0.84 | 56 | B4P, LYN, MG |
| 4 | 583 | 0.76 | 0.83 | 60 | B4P, LYN, MG |
| 5 | 567 | 0.75 | 0.82 | 59 | B4P, LYN, MG |
Interfaces
5 interfaces between chains.
- C–D · 4480 Ų buried · 83 hydrogen bonds · protein-protein
- A–B · 4468 Ų buried · 82 hydrogen bonds · protein-protein
- A–D · 341 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 249 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 70 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3A74 · Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with Diadenosine… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9RHV9 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase (Q9RHV9) · a predicted model of the same protein · chain D 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 Q9RHV9
- Elsewhere: RCSB PDB 3A74 · PDBe 3A74 · UniProt Q9RHV9
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