Research workbench
Cryo-EM structure of the unliganded msmo-PGS2 in a lipidic environment
Analyse Cryo-EM structure of the unliganded msmo-PGS2 in a lipidic environment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CXO
- Type
- protein
- Length
- 551 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Smoothened homolog, glga glycogen synthase chimera
- UniProt
- P56726, Q9V2J8
- Ligands
- CLR
- Pockets
- 5 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Smoothened homolog, glga glycogen synthase chimera | protein | 551 | 58% helix, 9% strand | P56726, Q9V2J8 |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.77 | 0.99 | 23 | empty |
| 2 | 347 | 0.76 | 0.86 | 42 | empty |
| 3 | 415 | 0.69 | 0.81 | 51 | empty |
| 4 | 391 | 0.62 | 0.77 | 45 | empty |
| 5 | 98 | 0.40 | 0.76 | 18 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 8CXO · Cryo-EM structure of the unliganded mSMO-PGS2 in a lipidic environment · the same entry in another collection · chain A against A, TM-score 1.00
- P56726 · AlphaFold monomer V2.0 prediction for smoothened homolog (P56726) · a predicted model of the same protein · chain A against A, TM-score 0.62
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 P56726
- Every structure of UniProt Q9V2J8
- Elsewhere: RCSB PDB 8CXO · PDBe 8CXO · UniProt P56726 · UniProt Q9V2J8
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