SMTL ID : 7qa8.1

Structure of the GPCR dimer Ste2 bound to an antagonist

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: N.25, T.35 No protein-ligand interaction detected (PLIP) NAG.2: 1 residues within 4Å: Chain A: N.32 No protein-ligand interaction detected (PLIP) NAG.20: 1 residues within 4Å: Chain D: N.32 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain D: N.25, T.35 No protein-ligand interaction detected (PLIP)

34 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)(Non-functional Binders)

Y01.3: 4 residues within 4Å: Chain A: F.182, I.190 Ligands: Y01.10, Y01.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.182, A:I.190 Y01.4: 10 residues within 4Å: Chain A: L.247, S.251, Q.253, L.291 Chain D: I.67, M.71 Ligands: Y01.5, Y01.7, Y01.22, Y01.32 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.247, A:L.291, D:I.67 Y01.5: 12 residues within 4Å: Chain A: T.72, R.74, L.287, S.288, L.291, M.294 Chain D: L.64, I.67, R.74 Ligands: Y01.4, Y01.7, Y01.12 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:I.67, A:L.287 Salt bridges: D:R.74, A:R.74 Y01.6: 5 residues within 4Å: Chain A: T.172, Y.203, L.210 Ligands: Y01.16, Y01.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.172, A:Y.203, A:L.210 Hydrogen bonds: A:Y.203 Y01.7: 12 residues within 4Å: Chain A: V.257, I.261, N.271, Q.272, G.273, V.276, L.277, L.284 Ligands: Y01.4, Y01.5, Y01.12, Y01.22 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.257, A:I.261, A:V.276, A:L.277, A:L.284 Hydrogen bonds: A:N.271, A:G.273 Y01.8: 9 residues within 4Å: Chain A: L.66, I.67, W.70, M.71, F.89, I.92 Ligands: Y01.14, Y01.17, Y01.26 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.66, A:I.67, A:W.70, A:W.70, A:F.89, A:I.92 Y01.9: 6 residues within 4Å: Chain A: W.70, R.76, K.77, V.86, F.89 Ligands: Y01.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.70, A:W.70, A:V.86, A:F.89 Salt bridges: A:R.76, A:K.77 Y01.10: 5 residues within 4Å: Chain A: F.182, V.183, V.186 Ligands: Y01.3, Y01.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.182, A:V.183, A:V.186 Y01.11: 6 residues within 4Å: Chain A: I.209, S.213, Y.266, S.267 Chain C: H.1 Ligands: Y01.19 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Salt bridges: C:H.1 Hydrophobic interactions: A:I.209, A:I.209 Y01.12: 8 residues within 4Å: Chain A: T.50, V.280, L.284 Chain D: F.99, L.103 Ligands: Y01.5, Y01.7, Y01.22 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:F.99, D:L.103, A:T.50, A:V.280, A:L.284 Hydrogen bonds: A:T.50 Y01.13: 7 residues within 4Å: Chain A: F.89, R.122, G.123, H.126 Ligands: Y01.9, Y01.14, Y01.15 No protein-ligand interaction detected (PLIP) Y01.14: 5 residues within 4Å: Chain A: L.93, K.100, S.121 Ligands: Y01.8, Y01.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.93 Hydrogen bonds: A:S.121 Salt bridges: A:K.100 Y01.15: 7 residues within 4Å: Chain A: R.122, H.126, A.130, I.133, Y.193 Ligands: Y01.13, Y01.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.133, A:I.133 Salt bridges: A:R.122 Y01.16: 6 residues within 4Å: Chain A: T.172, I.175, T.179, Y.203 Ligands: Y01.6, Y01.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.172, A:I.175, A:T.179, A:Y.203 Salt bridges: A:K.187 Y01.17: 7 residues within 4Å: Chain A: A.63, K.100, L.103 Ligands: Y01.8, Y01.26, Y01.36, Y01.37 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.63, A:K.100 Hydrogen bonds: A:L.103 Salt bridges: A:K.100, A:K.100 Y01.18: 6 residues within 4Å: Chain A: I.133, I.190, Y.193, N.194 Ligands: Y01.3, Y01.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.133, A:I.190, A:Y.193 Hydrogen bonds: A:N.194 Y01.19: 9 residues within 4Å: Chain A: D.201, K.202, N.205, A.206, I.209, S.213 Chain C: H.1 Ligands: Y01.6, Y01.11 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:K.202, A:A.206, A:I.209, A:I.209 Hydrogen bonds: A:N.205, C:H.1 Salt bridges: C:H.1 Y01.22: 7 residues within 4Å: Chain D: A.63, K.100, L.103 Ligands: Y01.4, Y01.7, Y01.12, Y01.32 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:A.63, D:K.100 Hydrogen bonds: D:L.103 Salt bridges: D:K.100 Y01.23: 5 residues within 4Å: Chain D: H.126, I.134, Y.193 Ligands: Y01.31, Y01.38 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.134 Y01.24: 6 residues within 4Å: Chain D: T.172, I.175, K.187, Y.203 Ligands: Y01.25, Y01.34 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:T.172, D:I.175, D:Y.203 Salt bridges: D:K.187 Y01.25: 7 residues within 4Å: Chain D: T.172, L.173, M.180, K.202, Y.203 Ligands: Y01.24, Y01.28 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.173, D:Y.203 Hydrogen bonds: D:Y.203 Salt bridges: D:K.202, D:K.202 Y01.26: 10 residues within 4Å: Chain A: I.67, M.71 Chain D: L.247, S.251, Q.253, L.291 Ligands: Y01.8, Y01.17, Y01.27, Y01.36 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.247, D:L.291, A:I.67 Y01.27: 11 residues within 4Å: Chain A: L.64, I.67, M.71 Chain D: T.72, R.74, L.284, L.287, S.288, L.291, M.294 Ligands: Y01.26 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:I.67, A:M.71, D:L.284, D:L.287, D:L.291, D:L.291 Salt bridges: D:R.74 Y01.28: 7 residues within 4Å: Chain D: L.173, K.202, A.206, I.209, L.210 Ligands: Y01.25, Y01.35 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.173, D:A.206, D:I.209, D:L.210 Salt bridges: D:K.202 Y01.29: 5 residues within 4Å: Chain D: L.93, A.96, K.100 Ligands: Y01.31, Y01.32 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.93, D:A.96 Salt bridges: D:K.100 Y01.30: 4 residues within 4Å: Chain D: F.182, I.190 Ligands: Y01.34, Y01.38 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.182, D:I.190 Y01.31: 8 residues within 4Å: Chain D: F.89, L.93, L.97, R.122, G.123, H.126 Ligands: Y01.23, Y01.29 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.97, D:H.126 Salt bridges: D:H.126 Y01.32: 6 residues within 4Å: Chain D: W.70, M.71, F.89 Ligands: Y01.4, Y01.22, Y01.29 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.70, D:F.89 Y01.33: 5 residues within 4Å: Chain D: W.70, R.76, K.77, V.86, F.89 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.70, D:W.70, D:V.86 Salt bridges: D:R.76, D:K.77 Y01.34: 2 residues within 4Å: Ligands: Y01.24, Y01.30 No protein-ligand interaction detected (PLIP) Y01.35: 4 residues within 4Å: Chain B: H.1 Chain D: N.216, Y.266 Ligands: Y01.28 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:N.216, D:Y.266 Salt bridges: B:H.1 Y01.36: 8 residues within 4Å: Chain D: Q.272, G.273, V.276, L.277, L.284 Ligands: Y01.17, Y01.26, Y01.37 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.276, D:L.284 Y01.37: 8 residues within 4Å: Chain A: L.103 Chain D: T.50, M.54, V.276, V.280, L.287 Ligands: Y01.17, Y01.36 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.280, D:L.287 Y01.38: 4 residues within 4Å: Chain D: L.137, M.189 Ligands: Y01.23, Y01.30 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.137

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
HIS-ALA-LEU-GLN-LEU-LYS-PRO-GLY-GLN-PRO-NLE-TYR: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

B
K

C
I

Membrane

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

HIS-ALA-LEU-GLN-LEU-LYS-PRO-GLY-GLN-PRO-NLE-TYR

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