SMTL ID : 7cum.1

Cryo-EM structure of human GABA(B) receptor bound to the antagonist CGP54626

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x 2BV: (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropyl]phosphinic acid(Non-covalent)

2BV.1: 10 residues within 4Å: Chain A: G.43, W.44, C.108, S.109, G.130, S.132, H.149, W.257, G.325, E.328 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.44, A:W.257, A:W.257 Hydrogen bonds: A:S.109, A:S.132, A:S.132, A:S.132, A:E.328, A:E.328

2 x UNL: UNKNOWN LIGAND

UNL.2: 35 residues within 4Å: Chain A: L.449, C.499, A.502, L.509, G.510, D.512, C.525, R.528, L.529, L.532, G.533, F.536, W.590, L.596, H.622, C.623, L.632, F.635, Y.636, K.639, G.640, L.643, V.674, C.678, L.679, T.681, A.682, T.685, S.689, F.696, A.699, A.702, I.703, S.706, S.707 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.529, A:F.536, A:F.536, A:F.635, A:Y.636, A:A.682, A:I.703 Hydrogen bonds: A:L.509, A:R.528, A:R.528, A:C.623, A:C.623 Salt bridges: A:R.528 UNL.8: 32 residues within 4Å: Chain B: S.530, F.537, G.538, D.540, F.549, R.556, T.557, L.560, T.561, Y.564, W.615, L.621, E.646, H.647, C.648, L.657, V.660, Y.661, K.664, V.699, C.703, I.704, G.706, A.707, S.710, Q.720, V.724, V.727, I.728, C.731, S.732, T.735 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.564, B:K.664, B:V.699, B:I.704, B:I.728 Hydrogen bonds: B:D.540, B:C.648, B:S.710 Salt bridges: B:R.556, B:H.647

16 x CLR: CHOLESTEROL(Non-covalent)(Non-functional Binders)(Covalent)

CLR.3: 6 residues within 4Å: Chain A: I.647, Y.651, K.654, M.669, Y.672, V.676 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.651, A:Y.672, A:Y.672, A:Y.672 CLR.4: 9 residues within 4Å: Chain A: W.548, W.549, K.571, T.575, L.578, L.641, L.642, L.645 Ligands: CLR.19 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.548, A:W.549, A:T.575, A:L.578, A:L.641, A:L.645 CLR.5: 10 residues within 4Å: Chain A: G.640, L.644, L.679, P.683, M.686, I.687 Chain B: L.666 Ligands: CLR.6, CLR.11, CLR.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.644 CLR.6: 10 residues within 4Å: Chain A: N.629, T.630, G.633, I.634, G.637, Y.638, L.641 Ligands: CLR.5, CLR.12, CLR.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.634, A:Y.638 CLR.7: 7 residues within 4Å: Chain A: L.644, F.648, Y.651 Chain B: W.576, L.666, F.670 Ligands: CLR.14 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.644, A:F.648, A:Y.651, A:Y.651, B:W.576, B:F.670 CLR.9: 4 residues within 4Å: Chain B: H.652, I.655, W.656 Ligands: CLR.10 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.655 CLR.10: 4 residues within 4Å: Chain B: I.655, I.659 Ligands: CLR.9, CLR.11 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.655, B:I.655, B:I.659 CLR.11: 9 residues within 4Å: Chain A: I.687 Chain B: T.654, I.655, I.659, A.662, L.666 Ligands: CLR.5, CLR.10, CLR.12 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.655, B:A.662 CLR.12: 9 residues within 4Å: Chain A: L.641 Chain B: T.654, A.662, G.665, L.666, F.711 Ligands: CLR.5, CLR.6, CLR.11 No protein-ligand interaction detected (PLIP) CLR.13: 3 residues within 4Å: Chain B: F.711, L.712 Ligands: CLR.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.711, B:F.711 Hydrogen bonds: B:F.711 CLR.14: 8 residues within 4Å: Chain B: F.572, W.576, I.600, M.604, I.607, Y.663, F.670 Ligands: CLR.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.600, B:I.607, B:I.607, B:Y.663, B:Y.663 Hydrogen bonds: B:W.576 CLR.15: 3 residues within 4Å: Chain B: L.491, M.495, L.744 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.495, B:L.744 CLR.16: 2 residues within 4Å: Chain B: V.741, I.745 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.741, B:I.745 CLR.17: 3 residues within 4Å: Chain B: M.694, I.701 Ligands: CLR.18 No protein-ligand interaction detected (PLIP) CLR.18: 4 residues within 4Å: Chain B: W.676, I.701 Ligands: CLR.17, CLR.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.701 CLR.19: 7 residues within 4Å: Chain A: W.548, L.641 Chain B: L.669, W.676, R.679 Ligands: CLR.4, CLR.18 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.676, B:W.676, A:L.641

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Structural Basis for Activation of the Heterodimeric GABA B Receptor. J.Mol.Biol. (2020)

Release Date

2020-11-11

Peptides

Gamma-aminobutyric acid type B receptor subunit 1: A
Gamma-aminobutyric acid type B receptor subunit 2: B

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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Gamma-aminobutyric acid type B receptor subunit 1

Gamma-aminobutyric acid type B receptor subunit 2

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