Research workbench
Crystal structure of L-glutamate and ampcpp bound to glutamine aminoacyl tRNA synthetase
Analyse Crystal structure of L-glutamate and ampcpp bound to glutamine aminoacyl tRNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O0C
- 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
- GLU, AMP, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% 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 | 32% helix, 25% strand | P00962 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · chains B, A
- AMP · Adenosine monophosphate · 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.78 | 0.95 | 23 | empty |
| 2 | 790 | 0.75 | 0.80 | 71 | SO4, GLU, AMP |
| 3 | 140 | 0.68 | 0.89 | 23 | empty |
| 4 | 654 | 0.65 | 0.76 | 39 | empty |
| 5 | 585 | 0.64 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- B–A · 2661 Ų buried · 65 hydrogen bonds · protein-nucleic
Compared structures
- 1O0C · Crystal structure of L-glutamate and ampcpp bound to glutamine aminoacyl tRNA synthetase · 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 1O0C · PDBe 1O0C · UniProt P00962
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