Research workbench
Sidekick-1 immunoglobulin domains 1-5
Analyse Sidekick-1 immunoglobulin domains 1-5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K6W
- Type
- protein
- Length
- 950 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Mus musculus
- Molecule
- Protein sidekick-1
- UniProt
- Q3UH53
- Ligands
- NAG, FUC, SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · resolution 3.5 · 1 distinct chain · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein sidekick-1 | protein | 475 | 5% helix, 54% strand | Q3UH53 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.80 | 0.84 | 58 | GOL |
| 2 | 807 | 0.75 | 0.79 | 76 | GOL |
| 3 | 1069 | 0.72 | 0.76 | 79 | SO4 |
| 4 | 92 | 0.60 | 0.87 | 19 | empty |
| 5 | 67 | 0.32 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1509 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 8 disulfide (N-glycosylation, disulfide).
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 Q3UH53
- Elsewhere: RCSB PDB 5K6W · PDBe 5K6W · UniProt Q3UH53
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