SMTL ID : 7qb9.1

Structure of the ligand-free GPCR dimer Ste2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

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.14: 2 residues within 4Å: Chain B: N.25, T.35 No protein-ligand interaction detected (PLIP) NAG.15: 1 residues within 4Å: Chain B: N.32 No protein-ligand interaction detected (PLIP)

22 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 9 residues within 4Å: Chain A: L.247, S.251, L.291 Chain B: I.67, M.71 Ligands: Y01.4, Y01.6, Y01.16, Y01.23 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.247, A:L.291, A:L.291, B:I.67 Y01.4: 13 residues within 4Å: Chain A: T.65, T.72, L.287, S.288, L.291, M.294 Chain B: L.64, I.67, M.71, R.74 Ligands: Y01.3, Y01.6, Y01.9 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.65, A:T.72, A:L.291, B:L.64, B:I.67, B:M.71 Salt bridges: B:R.74 Y01.5: 7 residues within 4Å: Chain A: A.96, K.100 Ligands: Y01.7, Y01.11, Y01.19, Y01.25, Y01.26 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.96 Salt bridges: A:K.100, A:K.100 Y01.6: 10 residues within 4Å: Chain A: I.261, N.271, Q.272, G.273, V.276, L.277 Ligands: Y01.3, Y01.4, Y01.9, Y01.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.261, A:V.276, A:L.277 Hydrogen bonds: A:N.271 Y01.7: 8 residues within 4Å: Chain A: L.66, I.67, W.70, M.71, R.76, F.89 Ligands: Y01.5, Y01.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.66, A:I.67, A:W.70, A:F.89 Salt bridges: A:R.76 Y01.8: 6 residues within 4Å: Chain A: W.70, R.76, K.77, V.86, F.89 Ligands: Y01.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.70, A:V.86, A:F.89 Salt bridges: A:R.76, A:K.77, A:K.77 Y01.9: 6 residues within 4Å: Chain A: T.50, A.61 Chain B: L.103 Ligands: Y01.4, Y01.6, Y01.16 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.50, A:A.61, B:L.103 Y01.10: 7 residues within 4Å: Chain A: F.89, R.122, G.123, H.126 Ligands: Y01.8, Y01.11, Y01.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.89 Salt bridges: A:H.126, A:H.126 Y01.11: 6 residues within 4Å: Chain A: F.89, L.93, K.100 Ligands: Y01.5, Y01.7, Y01.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.89, A:L.93, A:K.100 Salt bridges: A:K.100 Y01.12: 5 residues within 4Å: Chain A: H.126, I.134, M.189, Y.193 Ligands: Y01.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.134 Y01.13: 4 residues within 4Å: Chain A: I.133, M.189, Y.193, N.194 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.133, A:Y.193 Hydrogen bonds: A:N.194 Y01.16: 9 residues within 4Å: Chain B: A.63, A.96, K.100, L.103 Ligands: Y01.3, Y01.6, Y01.9, Y01.21, Y01.23 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.63, B:A.96, B:K.100, B:L.103 Hydrogen bonds: B:L.103 Salt bridges: B:K.100, B:K.100 Y01.17: 6 residues within 4Å: Chain B: H.126, I.134, M.189, Y.193 Ligands: Y01.18, Y01.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.134 Y01.18: 2 residues within 4Å: Chain B: L.137 Ligands: Y01.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.137 Y01.19: 8 residues within 4Å: Chain A: I.67, M.71 Chain B: F.244, L.247, S.251, L.291 Ligands: Y01.5, Y01.20 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.67, B:L.247 Y01.20: 12 residues within 4Å: Chain A: L.64, I.67, M.71 Chain B: T.65, T.72, R.74, L.284, L.287, S.288, L.291, M.294 Ligands: Y01.19 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.65, B:T.72, B:R.74, B:L.284, B:L.291, A:L.64, A:I.67, A:M.71 Y01.21: 6 residues within 4Å: Chain B: L.93, A.96, K.100 Ligands: Y01.16, Y01.22, Y01.23 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.93, B:A.96 Salt bridges: B:K.100 Y01.22: 7 residues within 4Å: Chain B: F.89, L.93, R.122, G.123, H.126 Ligands: Y01.17, Y01.21 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.89, B:L.93, B:H.126 Y01.23: 9 residues within 4Å: Chain B: L.66, I.67, W.70, M.71, F.89, I.92 Ligands: Y01.3, Y01.16, Y01.21 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.66, B:I.67, B:W.70, B:F.89, B:I.92 Y01.24: 5 residues within 4Å: Chain B: W.70, R.76, K.77, V.86, F.89 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.70, B:F.89, B:F.89 Salt bridges: B:K.77, B:K.77 Y01.25: 9 residues within 4Å: Chain B: I.261, N.271, Q.272, G.273, V.276, L.277, L.284 Ligands: Y01.5, Y01.26 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.261, B:V.276, B:L.277, B:L.284 Y01.26: 6 residues within 4Å: Chain A: L.103 Chain B: T.50, M.54, A.61 Ligands: Y01.5, Y01.25 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.61, A:L.103

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

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

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