Research workbench
Cryo-EM structure of SCAP/INSIG complex in the present of digitonin.
Analyse Cryo-EM structure of SCAP/INSIG complex in the present of digitonin. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ETW
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-induced gene 2 protein; Sterol regulatory element-binding protein cleavage…
- UniProt
- Q9Y5U4, Q12770
- Ligands
- AJP, NAG
- Pockets
- 14 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 56% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-induced gene 2 protein | protein | 197 | 69% helix, 0% strand | Q9Y5U4 |
| B | Sterol regulatory element-binding protein cleavage- activating protein | protein | 483 | 51% helix, 7% strand | Q12770 |
Ligands and binding sites
- AJP · Digitonin · ligand · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.80 | 0.82 | 104 | empty |
| 2 | 1115 | 0.79 | 0.80 | 87 | empty |
| 3 | 892 | 0.75 | 0.78 | 68 | AJP |
| 4 | 500 | 0.69 | 0.79 | 75 | empty |
| 5 | 337 | 0.64 | 0.79 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 1205 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 7ETW · Cryo-EM structure of Scap/Insig complex in the present of digitonin. · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5U4 · AlphaFold monomer V2.0 prediction for insulin-induced gene 2 protein (Q9Y5U4) · a predicted model of the same protein · chain A against A, TM-score 0.85
- Q12770 · AlphaFold monomer V2.0 prediction for sterol regulatory element- binding protein… · a predicted model of the same protein · chain B against A, TM-score 0.52
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 Q9Y5U4
- Every structure of UniProt Q12770
- Elsewhere: RCSB PDB 7ETW · PDBe 7ETW · UniProt Q9Y5U4 · UniProt Q12770
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