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Class D GPCR STE2 dimer coupled to two G proteins

Analyse Class D GPCR STE2 dimer coupled to two G proteins in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AD3
Type: protein
Length: 1,202 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pheromone alpha factor receptor; Alpha-factor mating pheromone; STE4 isoform 1; Guanine…
UniProt: P0CI39, A0A6A5Q727, P08539, A0A6A5PT44
Ligands: Y01, NAG
Pockets: 17 · best druggability 0.81

Structure

electron microscopy · 6 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Pheromone alpha factor receptor	protein	298	74% helix, 2% strand	P0CI39
K, I	Alpha-factor mating pheromone	protein	13	0% helix, 0% strand	—
F	STE4 isoform 1	protein	318	2% helix, 36% strand	A0A6A5Q727
E	Guanine nucleotide-binding protein alpha-1 SUBUNIT,GUANINE nucleotide-binding protein alpha-1 subunit	protein	216	41% helix, 14% strand	P08539
G	Guanine nucleotide-binding protein subunit gamma	protein	23	57% helix, 0% strand	A0A6A5PT44
H	Guanine nucleotide-binding protein alpha-1 SUBUNIT,GUANINE nucleotide-binding protein alpha-1 subunit	protein	23	83% helix, 0% strand	P08539

Ligands and binding sites

Y01 · Cholesterol hemisuccinate · ligand · 6 copies · chains B, A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	262	0.81	0.93	30	empty
2	397	0.80	0.89	43	empty
3	591	0.70	0.78	61	empty
4	232	0.67	0.84	37	empty
5	158	0.61	0.84	40	empty

Interfaces

7 interfaces between chains.

B–A · 2609 Å² buried · 13 hydrogen bonds · protein-protein
F–E · 1575 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 1242 Å² buried · 8 hydrogen bonds · protein-protein
B–K · 1189 Å² buried · 15 hydrogen bonds · protein-protein
A–I · 1149 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 glycan (N-glycosylation).

Compared structures

7AD3 · Class D GPCR Ste2 dimer coupled to two G proteins · the same entry in another collection · chain H against H, TM-score 1.00
P0CI39 · AlphaFold monomer V2.0 prediction for pheromone alpha factor receptor (P0CI39) · a predicted model of the same protein · chain B against A, TM-score 0.92
P08539 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein alpha-1 subunit… · a predicted model of the same protein · chain E against A, TM-score 0.79

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
Every structure of UniProt A0A6A5Q727
Every structure of UniProt P08539
Every structure of UniProt A0A6A5PT44
Elsewhere: RCSB PDB 7AD3 · PDBe 7AD3 · UniProt P0CI39 · UniProt A0A6A5Q727 · UniProt P08539 · UniProt A0A6A5PT44

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