Research workbench
Crystal structure of AQ_298
Analyse Crystal structure of AQ_298 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DQ3
- Type
- protein
- Length
- 850 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Seryl-tRNA synthetase
- EC
- 6.1.1.11
- UniProt
- O66647
- Ligands
- SSA
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Seryl-tRNA synthetase (EC 6.1.1.11) | protein | 425 | 43% helix, 21% strand | O66647 |
Ligands and binding sites
- SSA · 5'-O-(N-(L-seryl)-sulfamoyl)adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.85 | 0.96 | 53 | empty |
| 2 | 596 | 0.75 | 0.82 | 50 | SSA |
| 3 | 677 | 0.75 | 0.81 | 58 | SSA |
| 4 | 145 | 0.44 | 0.75 | 23 | empty |
| 5 | 120 | 0.43 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2386 Ų buried · 67 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
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 O66647
- Elsewhere: RCSB PDB 2DQ3 · PDBe 2DQ3 · UniProt O66647
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