MolNFT v1 · #29803 · protein + RNA
Glutaminyl-tRNA synthetase complexed to glutamine and 2'DEOXY A76 glutamine tRNA
1ZJW: “Glutaminyl-tRNA synthetase complexed to glutamine and 2'DEOXY A76 glutamine tRNA”. X-ray diffraction, 3 ligands (AMP, GLN, SO4), 7 pockets (best druggability 0.78). MolNFT v1 #29803 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1ZJW
- Type
- protein + RNA
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaminyl-tRNA; Glutaminyl-tRNA synthetase
- EC
- 6.1.1.18
- UniProt
- P00962
- Ligands
- AMP, GLN, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glutaminyl-tRNA | rna | 74 | — | — |
| A | Glutaminyl-tRNA synthetase (EC 6.1.1.18) | protein | 529 | 33% helix, 25% strand | P00962 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains B, A
- GLN · Glutamine · ligand · chains B, A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.78 | 0.96 | 25 | empty |
| 2 | 773 | 0.76 | 0.81 | 65 | SO4, AMP, GLN |
| 3 | 600 | 0.65 | 0.76 | 31 | empty |
| 4 | 582 | 0.65 | 0.77 | 34 | empty |
| 5 | 128 | 0.64 | 0.87 | 24 | empty |
Interfaces
1 interface between chains.
- B–A · 2680 Ų buried · 62 hydrogen bonds · protein-nucleic
Compared structures
- 1ZJW · Glutaminyl-tRNA synthetase complexed to glutamine and 2'deoxy A76 glutamine tRNA · the same entry in another collection · chain A against A, 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 0.99
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 1ZJW · PDBe 1ZJW · UniProt P00962
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