MolNFT v1 · #5932 · protein + RNA
Crystal structure of a tight-binding glutamine tRNA bound to glutamine aminoacyl tRNA synthetase
1EXD · Glutamine tRNA aptamer: “Crystal structure of a tight-binding glutamine tRNA bound to glutamine aminoacyl tRNA synthetase”. X-ray diffraction, 2 ligands (A, SO4), 8 pockets (best druggability 0.75). MolNFT v1 #5932 on GenesisL1: 3D…
- PDB
- 1EXD
- Type
- protein + RNA
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine tRNA aptamer; Glutaminyl-tRNA synthetase
- EC
- 6.1.1.18
- UniProt
- P00962
- Ligands
- A, SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glutamine tRNA aptamer | rna | 73 | — | — |
| A | Glutaminyl-tRNA synthetase (EC 6.1.1.18) | protein | 529 | 31% helix, 23% strand | P00962 |
Ligands and binding sites
- A · Adenosine-5'-monophosphate · ligand · chains B, A
- SO4 · Sulfate ion · ion · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.75 | 0.95 | 22 | empty |
| 2 | 792 | 0.75 | 0.80 | 70 | SO4, A |
| 3 | 606 | 0.67 | 0.77 | 30 | empty |
| 4 | 129 | 0.66 | 0.88 | 25 | empty |
| 5 | 615 | 0.65 | 0.76 | 36 | SO4 |
Interfaces
1 interface between chains.
- B–A · 2663 Ų buried · 63 hydrogen bonds · protein-nucleic
Compared structures
- 1EXD · Crystal structure of a tight-binding glutamine tRNA bound to glutamine aminoacyl tRNA… · the same entry in another collection · chain B against B, TM-score 1.00
- P00962 · AlphaFold monomer V2.0 prediction for glutamine--tRNA ligase (P00962) · a predicted model of the same protein · chain A 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 P00962
- Elsewhere: RCSB PDB 1EXD · PDBe 1EXD · UniProt P00962
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.