Research workbench
Quaternary complex of wild type 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 wild type E. COLI leucyl-tRNA synthetase with TRNA(LEU)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ONH
- Type
- protein + RNA
- Length
- 1,884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine--tRNA ligase; L-leucyl-TRNA(LEU)
- EC
- 6.1.1.4
- UniProt
- P07813
- Ligands
- LSS, VRT, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 860 | 37% helix, 22% strand | P07813 |
| B | L-leucyl-TRNA(LEU) | rna | 82 | — | — |
| E | L-leucyl-TRNA(LEU) | rna | 82 | — | — |
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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.84 | 0.85 | 82 | LSS |
| 2 | 244 | 0.82 | 0.95 | 32 | LSS |
| 3 | 984 | 0.81 | 0.82 | 94 | empty |
| 4 | 1047 | 0.79 | 0.81 | 82 | VRT |
| 5 | 784 | 0.77 | 0.81 | 61 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3070 Ų buried · 51 hydrogen bonds · protein-nucleic
- D–E · 3007 Ų buried · 51 hydrogen bonds · protein-nucleic
- A–D · 618 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 50 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 5ONH · Quaternary complex of wild type 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 0.90
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 5ONH · PDBe 5ONH · UniProt P07813
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