MolNFT v1 · #85892 · protein + RNA
Ternary complex of E. COLI leucyl-tRNA synthetase, TRNA(LEU) and leucyl-adenylate analogue in the aminoacylation conformation
4AQ7 · Leucine--tRNA ligase: “Ternary complex of E. COLI leucyl-tRNA synthetase, TRNA(LEU) and leucyl-adenylate analogue in the…”. X-ray diffraction, 4 ligands (LMS, LEU, ZN), 20 pockets (best druggability 0.82). MolNFT v1 #85892 on…
- PDB
- 4AQ7
- Type
- protein + RNA
- Length
- 1,874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine--tRNA ligase; E. COLI trnaleu uaa isoacceptor
- EC
- 6.1.1.4
- UniProt
- P07813
- Ligands
- LMS, LEU, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 860 | 39% helix, 23% strand | P07813 |
| B | E. COLI trnaleu uaa isoacceptor | rna | 78 | — | — |
| E | E. COLI trnaleu uaa isoacceptor | rna | 76 | — | — |
Ligands and binding sites
- LMS · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydro-2-furanyl]methyl sulfamate · ligand · 2 copies · chains A, B, D, E
- LEU · Leucine · ligand · 2 copies · chains A, B, D, E
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.82 | 0.94 | 33 | LMS, LEU |
| 2 | 1150 | 0.81 | 0.82 | 87 | LMS, LEU |
| 3 | 1014 | 0.81 | 0.82 | 87 | empty |
| 4 | 1156 | 0.76 | 0.79 | 81 | empty |
| 5 | 686 | 0.75 | 0.81 | 78 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2934 Ų buried · 49 hydrogen bonds · protein-nucleic
- D–E · 2911 Ų buried · 52 hydrogen bonds · protein-nucleic
- A–D · 666 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4AQ7 · Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and leucyl-adenylate… · 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 4AQ7 · PDBe 4AQ7 · UniProt P07813
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