MolNFT v1 · #8196 · protein + RNA
Structural basis for transfer RNA aminoaceylation by escherichia COLI glutaminyl-tRNA synthetase
1GTS · Trnagln: “Structural basis for transfer RNA aminoaceylation by escherichia COLI glutaminyl-tRNA synthetase”. X-ray diffraction, 1 ligand (AMP), 8 pockets (best druggability 0.78). MolNFT v1 #8196 on GenesisL1: 3D structure, binding…
- PDB
- 1GTS
- Type
- protein + RNA
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trnagln; Protein (glutaminyl-tRNA synthetase (E.C.6.1.1.18))
- UniProt
- P00962
- Ligands
- AMP
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Trnagln | rna | 74 | — | — |
| A | Protein (glutaminyl-tRNA synthetase (E.C.6.1.1.18)) | protein | 529 | 32% helix, 24% strand | P00962 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.78 | 0.96 | 27 | empty |
| 2 | 815 | 0.76 | 0.81 | 66 | AMP |
| 3 | 684 | 0.67 | 0.76 | 37 | empty |
| 4 | 121 | 0.65 | 0.88 | 25 | empty |
| 5 | 578 | 0.63 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- B–A · 2712 Ų buried · 80 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1GTS · Structural basis for transfer RNA aminoaceylation by escherichia COLI glutaminyl-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 0.99
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 1GTS · PDBe 1GTS · UniProt P00962
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