MolNFT v1 · #96914 · protein + RNA
Crystal structure of E COLI E. COLI glutaminyl-tRNA synthetase bound to TRNA(GLN)(CUG) and ATP from novel cryostabilization conditions
4JXX · Glutamine--tRNA ligase: “Crystal structure of E COLI E. COLI glutaminyl-tRNA synthetase bound to TRNA(GLN)(CUG) and ATP from novel…”. X-ray diffraction, 2 ligands (ATP, SO4), 9 pockets (best druggability 0.76). MolNFT v1 #96914 on…
- PDB
- 4JXX
- Type
- protein + RNA
- Length
- 607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine--tRNA ligase; RNA (71-mer)
- EC
- 6.1.1.18
- UniProt
- P00962
- Ligands
- ATP, SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamine--tRNA ligase (EC 6.1.1.18) | protein | 536 | 31% helix, 25% strand | P00962 |
| B | RNA (71-mer) | rna | 71 | — | — |
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 | 866 | 0.76 | 0.80 | 68 | ATP, SO4 |
| 2 | 108 | 0.76 | 0.96 | 19 | empty |
| 3 | 929 | 0.71 | 0.77 | 50 | empty |
| 4 | 626 | 0.65 | 0.76 | 28 | empty |
| 5 | 211 | 0.61 | 0.81 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2740 Ų buried · 69 hydrogen bonds · protein-nucleic
Compared structures
- 4JXX · Crystal structure of E coli E. coli glutaminyl-tRNA synthetase bound to tRNA(Gln)(CUG)… · 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 4JXX · PDBe 4JXX · UniProt P00962
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