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Quaternary complex of mutant T252A of E. coli leucyl-tRNA synthetase with tRNA(leu), leucyl-adenylate analogue, and post-transfer editing analogue of norvaline in the aminoacylation conformation
Analyse Quaternary complex of mutant T252A of E. coli leucyl-tRNA synthetase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ON2
- Type
- protein + RNA
- Length
- 1,887 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Escherichia coli (strain K12); SYNTHETIC CONSTRUCT
- Molecule
- Leucine--tRNA ligase; tRNA(leu)
- EC
- 6.1.1.4
- UniProt
- P07813
- Ligands
- LSS, VRT, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 3.1 · 4 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 862 | 38% helix, 22% strand | P07813 |
| B | tRNA(leu) | rna | 85 | — | — |
| D | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 860 | 38% helix, 20% strand | P07813 |
| E | tRNA(leu) | rna | 80 | — | — |
Ligands and binding sites
- LSS · 5'-O-(L-leucylsulfamoyl)adenosine · ligand · 2 copies · chains A, B, D, E
- VRT · 2'-(L-norvalyl)amino-2'-deoxyadenosine · ligand · 2 copies · chains A, D
- ZN · Zinc ion · metal · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.82 | 0.95 | 31 | LSS |
| 2 | 1181 | 0.82 | 0.83 | 88 | LSS |
| 3 | 1049 | 0.80 | 0.81 | 78 | VRT |
| 4 | 882 | 0.78 | 0.81 | 74 | empty |
| 5 | 1186 | 0.75 | 0.79 | 68 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3058 Ų buried · 57 hydrogen bonds · protein-nucleic
- D–E · 3008 Ų buried · 50 hydrogen bonds · protein-nucleic
- A–D · 634 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 131 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5ON2 · Quaternary complex of mutant T252A of E. COLI leucyl-tRNA synthetase with TRNA(LEU)… · the same entry in another collection · chain A against A, TM-score 1.00
- P07813 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase (P07813) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 P07813
- Elsewhere: RCSB PDB 5ON2 · PDBe 5ON2 · UniProt P07813
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