Research workbench
Crystal structure of aspartyl-tRNA synthetase from sulfolobus tokodaii
Analyse Crystal structure of aspartyl-tRNA synthetase from sulfolobus tokodaii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WYD
- Type
- protein
- Length
- 857 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical aspartyl-tRNA synthetase
- UniProt
- Q976I3
- Ligands
- CL, SO4
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical aspartyl-tRNA synthetase | protein | 428 | 33% helix, 28% strand | Q976I3 |
| B | Hypothetical aspartyl-tRNA synthetase | protein | 429 | 33% helix, 28% strand | Q976I3 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.78 | 0.81 | 101 | CL, EPE |
| 2 | 751 | 0.78 | 0.82 | 81 | EPE |
| 3 | 94 | 0.59 | 0.87 | 30 | CL |
| 4 | 183 | 0.49 | 0.76 | 24 | empty |
| 5 | 180 | 0.49 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4350 Ų buried · 58 hydrogen bonds · protein-protein
Compared structures
- 1WYD · Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii · the same entry in another collection · chain A against A, TM-score 1.00
- Q976I3 · AlphaFold monomer V2.0 prediction for aspartate--TRNA(ASP/ASN) ligase (Q976I3) · a predicted model of the same protein · chain B 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 Q976I3
- Elsewhere: RCSB PDB 1WYD · PDBe 1WYD · UniProt Q976I3
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