Research workbench
Structure of the GPCR dimer STE2 in the inactive-like state bound to agonist
Analyse Structure of the GPCR dimer STE2 in the inactive-like state bound to agonist in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QBC
- Type
- protein
- Length
- 622 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pheromone alpha factor receptor; Alpha factor pheromone
- UniProt
- P0CI39
- Ligands
- Y01, NAG
- Pockets
- 6 · best druggability 0.65
Structure
electron microscopy · 2 distinct chains · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pheromone alpha factor receptor | protein | 298 | 69% helix, 2% strand | P0CI39 |
| I, K | Alpha factor pheromone | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 12 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 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 | 469 | 0.65 | 0.77 | 47 | Y01 |
| 2 | 476 | 0.63 | 0.76 | 47 | Y01 |
| 3 | 133 | 0.56 | 0.83 | 29 | empty |
| 4 | 122 | 0.53 | 0.82 | 27 | empty |
| 5 | 93 | 0.38 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2166 Ų buried · 10 hydrogen bonds · protein-protein
- K–B · 1222 Ų buried · 17 hydrogen bonds · protein-protein
- A–I · 1212 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 7QBC · Structure of the GPCR dimer Ste2 in the inactive-like state bound to agonist · the same entry in another collection · chain A against A, TM-score 1.00
- P0CI39 · AlphaFold monomer V2.0 prediction for pheromone alpha factor receptor (P0CI39) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P0CI39
- Elsewhere: RCSB PDB 7QBC · PDBe 7QBC · UniProt P0CI39
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