MolNFT v1 · #31099 · protein
Crystal structure of the editing domain of E. COLI leucyl-tRNA synthetase complexes with isoleucine
2AJI: “Crystal structure of the editing domain of E. COLI leucyl-tRNA synthetase complexes with isoleucine”. X-ray diffraction, 1 ligand (ILE), 4 pockets (best druggability 0.61). MolNFT v1 #31099 on GenesisL1: 3D structure, binding sites…
- PDB
- 2AJI
- Type
- protein
- Length
- 361 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-tRNA synthetase
- EC
- 6.1.1.4
- UniProt
- P07813
- Ligands
- ILE
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 186 | 29% helix, 24% strand | P07813 |
| B | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 175 | 28% helix, 25% strand | P07813 |
Ligands and binding sites
- ILE · Isoleucine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.61 | 0.78 | 29 | ILE |
| 2 | 175 | 0.49 | 0.77 | 23 | ILE |
| 3 | 69 | 0.40 | 0.79 | 14 | empty |
| 4 | 73 | 0.37 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 622 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2AJI · Crystal structure of the editing domain of E. coli leucyl-tRNA synthetase complexes with… · 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 B against A, TM-score 0.98
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 2AJI · PDBe 2AJI · UniProt P07813
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