SMTL ID : 7qbi.1

Structure of the GPCR dimer Ste2 in the active-like state bound to agonist

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 1 residues within 4Å: Chain A: N.25 No protein-ligand interaction detected (PLIP) NAG.2: 1 residues within 4Å: Chain A: N.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.32, A:N.32 NAG.11: 1 residues within 4Å: Chain D: N.32 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.32, D:N.32 NAG.12: 1 residues within 4Å: Chain D: N.25 No protein-ligand interaction detected (PLIP)

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 10 residues within 4Å: Chain A: C.59, I.92, A.96, F.99, K.100, L.103, S.104 Ligands: Y01.6, Y01.14, Y01.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.92, A:A.96, A:F.99 Hydrogen bonds: A:K.100 Salt bridges: A:K.100 Y01.4: 13 residues within 4Å: Chain A: N.46, T.50, I.53, M.54, V.57, Q.272, L.277, L.283 Chain D: G.60, A.63, L.103 Ligands: Y01.5, Y01.13 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:T.50, A:V.57, A:V.57, A:L.277, A:L.283, D:A.63 Hydrogen bonds: A:N.46 Y01.5: 4 residues within 4Å: Chain A: I.261, L.264 Ligands: Y01.4, Y01.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.261, A:L.264 Y01.6: 5 residues within 4Å: Chain A: I.92, L.93, K.100, G.123 Ligands: Y01.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.92, A:L.93, A:K.100 Salt bridges: A:K.100, A:K.100 Y01.7: 6 residues within 4Å: Chain A: K.202, A.206, I.209, L.210, S.213 Chain B: W.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.209, A:L.210 Y01.8: 4 residues within 4Å: Chain A: Y.266 Chain B: W.1, H.2, W.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.3, A:Y.266 Y01.9: 6 residues within 4Å: Chain C: W.3 Chain D: K.202, A.206, I.209, L.210, S.213 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.209, D:L.210 Y01.10: 3 residues within 4Å: Chain C: W.1, W.3 Chain D: Y.266 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.266, C:W.1, C:W.3 Y01.13: 8 residues within 4Å: Chain D: C.59, A.63, I.92, A.96, L.103 Ligands: Y01.4, Y01.5, Y01.16 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:A.63, D:I.92, D:A.96, D:L.103 Hydrogen bonds: D:L.103 Salt bridges: D:K.100 Y01.14: 11 residues within 4Å: Chain A: A.63, L.103 Chain D: N.46, T.50, I.53, M.54, Q.272, T.274, L.277 Ligands: Y01.3, Y01.15 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:A.63, A:L.103, D:T.50, D:T.274, D:L.277 Hydrogen bonds: D:N.46 Y01.15: 6 residues within 4Å: Chain D: I.261, L.264, L.268, L.277 Ligands: Y01.3, Y01.14 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.261, D:L.264, D:L.268, D:L.277 Y01.16: 5 residues within 4Å: Chain D: L.93, K.100, G.123, V.127 Ligands: Y01.13 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.93, D:K.100, D:V.127 Salt bridges: D:K.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Velazhahan, V. et al., Activation mechanism of the class D fungal GPCR dimer Ste2. Nature (2022)

Release Date

2022-03-16

Peptides

Pheromone alpha factor receptor: AD
Alpha factor pheromone: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

B
I

C
K

Membrane

We predict this structure to be a membrane protein.
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Pheromone alpha factor receptor

Alpha factor pheromone

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