Research workbench
Crystal structure of E. COLI glutaminyl-tRNA synthetase bound to ATP and native TRNA(GLN) containing the CMNM5S2U34 anticodon wobble base
Analyse Crystal structure of E. COLI glutaminyl-tRNA synthetase bound to ATP and native… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JYZ
- Type
- protein + RNA
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine--tRNA ligase; RNA (72-mer)
- EC
- 6.1.1.18
- UniProt
- P00962
- Ligands
- ATP, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamine--tRNA ligase (EC 6.1.1.18) | protein | 542 | 32% helix, 23% strand | P00962 |
| B | RNA (72-mer) | rna | 72 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.78 | 0.97 | 25 | empty |
| 2 | 726 | 0.75 | 0.80 | 62 | ATP, SO4 |
| 3 | 783 | 0.71 | 0.78 | 50 | empty |
| 4 | 571 | 0.64 | 0.76 | 29 | empty |
| 5 | 190 | 0.63 | 0.84 | 33 | SO4 |
Interfaces
1 interface between chains.
- A–B · 2754 Ų buried · 68 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 9 modified (nucleotide modification).
Compared structures
- 4JYZ · Crystal structure of E. coli glutaminyl-tRNA synthetase bound to ATP and native tRNA(Gln)… · 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 4JYZ · PDBe 4JYZ · UniProt P00962
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