Research workbench
Cryo-EM structure of SCAP/INSIG complex in the present of 25-hydroxyl cholesterol.
Analyse Cryo-EM structure of SCAP/INSIG complex in the present of 25-hydroxyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M49
- Type
- protein
- Length
- 420 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
- HC3
- Pockets
- 7 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-induced gene 2 protein | protein | 182 | 77% helix, 0% strand | Q9Y5U4 |
| B | Sterol regulatory element-binding protein cleavage- activating PROTEIN,STEROL regulatory element-binding protein cleavage-activating protein | protein | 238 | 79% helix, 0% strand | Q12770 |
Ligands and binding sites
- HC3 · 25-hydroxycholesterol · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.80 | 0.81 | 104 | HC3 |
| 2 | 423 | 0.70 | 0.81 | 45 | empty |
| 3 | 391 | 0.67 | 0.79 | 49 | empty |
| 4 | 134 | 0.65 | 0.87 | 28 | empty |
| 5 | 210 | 0.56 | 0.78 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1120 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6M49 · cryo-EM structure of Scap/Insig complex in the present of 25-hydroxyl cholesterol. · 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 0.90
- 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 0.77
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 6M49 · PDBe 6M49 · UniProt Q9Y5U4 · UniProt Q12770
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