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Structure of the GPCR dimer STE2 bound to an antagonist

Analyse Structure of the GPCR dimer STE2 bound to an antagonist in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QA8
Type: protein
Length: 622 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pheromone alpha factor receptor; His-ala-leu-gln-leu-lys-pro-gly-gln-pro-nle-tyr
UniProt: P0CI39
Ligands: Y01, NAG
Pockets: 6 · best druggability 0.69

Structure

electron microscopy · 2 distinct chains · 68% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pheromone alpha factor receptor	protein	299	71% helix, 4% strand	P0CI39
K, I	His-ala-leu-gln-leu-lys-pro-gly-gln-pro-nle-tyr	protein	12	0% helix, 0% strand	—

Ligands and binding sites

Y01 · Cholesterol hemisuccinate · ligand · 34 copies · chains A, B, I, K
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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	784	0.69	0.75	73	Y01
2	133	0.53	0.81	24	empty
3	120	0.52	0.81	24	empty
4	86	0.43	0.80	19	empty
5	92	0.42	0.78	16	empty

Interfaces

3 interfaces between chains.

A–B · 2159 Å² buried · 8 hydrogen bonds · protein-protein
A–I · 999 Å² buried · 9 hydrogen bonds · protein-protein
K–B · 998 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 2 modified (N-glycosylation, nonstandard).

Compared structures

7QA8 · Structure of the GPCR dimer Ste2 bound to an antagonist · 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 0.89

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 7QA8 · PDBe 7QA8 · UniProt P0CI39

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