Research workbench
Aspartyl tRNA synthetase from thermus thermophilus at 2.4 a resolution
Analyse Aspartyl tRNA synthetase from thermus thermophilus at 2.4 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G51
- Type
- protein
- Length
- 1,160 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartyl-tRNA synthetase
- EC
- 6.1.1.12
- UniProt
- P36419
- Ligands
- AMO, AMP, SO4
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartyl-tRNA synthetase (EC 6.1.1.12) | protein | 580 | 32% helix, 27% strand | P36419 |
Ligands and binding sites
- AMO · Aspartyl-adenosine-5'-monophosphate · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.79 | 0.98 | 20 | empty |
| 2 | 531 | 0.69 | 0.79 | 68 | SO4, AMO |
| 3 | 371 | 0.68 | 0.81 | 46 | SO4, AMO |
| 4 | 306 | 0.61 | 0.78 | 35 | empty |
| 5 | 234 | 0.54 | 0.77 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 5626 Ų buried · 90 hydrogen bonds · protein-protein
Compared structures
- 1G51 · Aspartyl tRNA synthetase from thermus thermophilus at 2.4 a resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P36419 · AlphaFold monomer V2.0 prediction for aspartate--TRNA(ASP) ligase (P36419) · 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 P36419
- Elsewhere: RCSB PDB 1G51 · PDBe 1G51 · UniProt P36419
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