Research workbench
Aspartyl-tRNA synthetase complexed with aspartic acid
Analyse Aspartyl-tRNA synthetase complexed with aspartic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NEL
- Type
- protein
- Length
- 876 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
- Q52428
- Ligands
- ASP
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartyl-tRNA synthetase (EC 6.1.1.12) | protein | 438 | 33% helix, 28% strand | Q52428 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.74 | 0.79 | 81 | empty |
| 2 | 563 | 0.69 | 0.78 | 70 | ASP |
| 3 | 381 | 0.67 | 0.81 | 48 | empty |
| 4 | 60 | 0.60 | 0.91 | 17 | empty |
| 5 | 81 | 0.49 | 0.83 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 4544 Ų buried · 83 hydrogen bonds · protein-protein
Compared structures
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 Q52428
- Elsewhere: RCSB PDB 3NEL · PDBe 3NEL · UniProt Q52428
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