SMTL ID : 7qbc.1

Structure of the GPCR dimer Ste2 in the inactive-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: 2 residues within 4Å: Chain A: T.23, N.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.23 NAG.2: 1 residues within 4Å: Chain A: N.32 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain D: T.23, N.25 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.23 NAG.10: 1 residues within 4Å: Chain D: N.32 No protein-ligand interaction detected (PLIP)

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 15 residues within 4Å: Chain A: T.65, T.72, R.74, C.252, L.284, L.287, L.291, M.294 Chain D: L.64, I.67, M.71, T.72 Ligands: Y01.6, Y01.12, Y01.13 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:L.64, D:I.67, D:M.71, A:T.65, A:T.72, A:L.284, A:L.287, A:L.291 Salt bridges: A:R.74, A:R.74 Y01.4: 7 residues within 4Å: Chain A: M.71 Chain D: L.247, S.251, L.291 Ligands: Y01.8, Y01.13, Y01.16 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.247, D:L.291 Y01.5: 7 residues within 4Å: Chain A: I.261, L.268, K.269, L.277 Ligands: Y01.6, Y01.11, Y01.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.261, A:L.268, A:L.277 Salt bridges: A:K.269 Y01.6: 12 residues within 4Å: Chain A: N.46, T.50, M.54, T.274, V.276 Chain D: C.59, L.64, F.99, L.103 Ligands: Y01.3, Y01.5, Y01.11 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:T.50, A:V.276, D:L.64, D:F.99, D:F.99, D:L.103 Y01.7: 8 residues within 4Å: Chain A: F.89, I.92, A.96, K.100, S.121, R.122, V.127 Ligands: Y01.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.89, A:I.92, A:A.96, A:K.100, A:V.127 Hydrogen bonds: A:S.121 Y01.8: 9 residues within 4Å: Chain A: A.96, F.99, K.100, L.103, S.104 Ligands: Y01.4, Y01.7, Y01.15, Y01.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.96, A:F.99, A:F.99 Y01.11: 8 residues within 4Å: Chain D: A.63, A.96, K.100, L.103 Ligands: Y01.5, Y01.6, Y01.12, Y01.14 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.63, D:A.96, D:K.100 Y01.12: 7 residues within 4Å: Chain A: L.247, S.251, L.291 Chain D: M.71 Ligands: Y01.3, Y01.5, Y01.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:S.251, A:L.291 Y01.13: 14 residues within 4Å: Chain A: L.64, I.67, M.71, T.72 Chain D: T.65, T.72, R.74, C.252, L.284, L.287, L.291, M.294 Ligands: Y01.3, Y01.4 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain D Hydrophobic interactions: A:L.64, A:I.67, A:M.71, D:T.65, D:T.72, D:R.74, D:L.284, D:L.287, D:L.291, D:L.291 Salt bridges: D:R.74, D:R.74 Y01.14: 9 residues within 4Å: Chain D: F.89, I.92, L.93, A.96, L.97, S.121, D.124, V.127 Ligands: Y01.11 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.92, D:L.93, D:L.93, D:A.96, D:L.97, D:V.127 Hydrogen bonds: D:S.121 Y01.15: 11 residues within 4Å: Chain A: G.60, L.64, F.99, L.103 Chain D: T.50, I.53, M.54, T.274, V.276 Ligands: Y01.8, Y01.16 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:I.53, D:V.276, A:L.64, A:L.64, A:F.99, A:L.103 Y01.16: 5 residues within 4Å: Chain D: I.261, K.269 Ligands: Y01.4, Y01.8, Y01.15 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.261 Salt bridges: D:K.269

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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