Research workbench
The structure of glutaminyl-tRNA synthetase from saccharomyces cerevisiae
Analyse The structure of glutaminyl-tRNA synthetase from saccharomyces cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H3S
- Type
- protein
- Length
- 585 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine-tRNA ligase
- EC
- 6.1.1.18
- UniProt
- P13188
- Ligands
- ZN, BR, CL
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamine-tRNA ligase (EC 6.1.1.18) | protein | 585 | 31% helix, 24% strand | P13188 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- BR · Bromide ion · ion · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 8 copies · chains A
- ACT · Acetate ion · additive · 4 copies · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.71 | 0.98 | 19 | empty |
| 2 | 478 | 0.68 | 0.79 | 51 | GOL, BR, ACT |
| 3 | 60 | 0.46 | 0.84 | 20 | GOL |
| 4 | 90 | 0.40 | 0.78 | 20 | empty |
| 5 | 55 | 0.38 | 0.79 | 16 | empty |
Compared structures
- 4H3S · The Structure of Glutaminyl-tRNA Synthetase from Saccharomyces Cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P13188 · AlphaFold monomer V2.0 prediction for glutamine--tRNA ligase (P13188) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P13188
- Elsewhere: RCSB PDB 4H3S · PDBe 4H3S · UniProt P13188
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