Research workbench
Lysyl-tRNA synthetase from bacillus stearothermophilus complexed with L-lysine hydroxamate-AMP
Analyse Lysyl-tRNA synthetase from bacillus stearothermophilus complexed with L-lysine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E9I
- 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
- XAH, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lysyl-tRNA synthetase (EC 6.1.1.6) | protein | 484 | 38% helix, 26% strand | Q9RHV9 |
Ligands and binding sites
- XAH · 5'-O-{(R)-hydroxy[(L-lysylamino)oxy]phosphoryl}adenosine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 4 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.84 | 0.98 | 57 | empty |
| 2 | 159 | 0.80 | 0.96 | 34 | empty |
| 3 | 561 | 0.76 | 0.83 | 63 | MG, XAH |
| 4 | 625 | 0.76 | 0.83 | 56 | MG, XAH |
| 5 | 629 | 0.76 | 0.82 | 55 | MG, XAH |
Interfaces
5 interfaces between chains.
- C–D · 4505 Ų buried · 79 hydrogen bonds · protein-protein
- A–B · 4505 Ų buried · 79 hydrogen bonds · protein-protein
- B–C · 563 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 340 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 76 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3E9I · Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with L-Lysine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RHV9 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase (Q9RHV9) · a predicted model of the same protein · chain A 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 3E9I · PDBe 3E9I · UniProt Q9RHV9
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