SMTL ID : 6wiv.1

Structure of human GABA(B) receptor in an inactive state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: D.87, L.362, N.365 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.362 Hydrogen bonds: A:D.87 NAG.2: 2 residues within 4Å: Chain A: N.385, I.388 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.388 NAG.3: 3 residues within 4Å: Chain A: N.397, F.410, A.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.397 NAG.10: 1 residues within 4Å: Chain B: N.404 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: G.277, E.309, E.423 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.277

1 x U3G: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-{[(9Z)-octadec-9-enoyl]oxy}propyl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)

U3G.5: 25 residues within 4Å: Chain A: T.516, C.520, A.523, L.530, G.531, R.549, L.550, L.553, G.554, F.557, G.560, M.564, E.642, H.643, C.644, M.649, F.656, Y.657, K.660, C.699, T.702, A.703, S.710, I.724, T.731 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.516, A:A.523, A:L.530, A:L.550, A:L.553, A:F.557, A:F.656, A:Y.657, A:K.660, A:K.660, A:T.702, A:A.703, A:I.724, A:T.731 Hydrogen bonds: A:G.531, A:R.549, A:C.644, A:S.710 Salt bridges: A:R.549, A:H.643

10 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 5 residues within 4Å: Chain A: N.650, T.651, G.654, I.655 Ligands: CLR.9 No protein-ligand interaction detected (PLIP) CLR.7: 5 residues within 4Å: Chain A: L.665, F.669, Y.672 Chain B: L.666 Ligands: CLR.12 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.665, A:L.665, A:F.669, A:Y.672, B:L.666 CLR.8: 3 residues within 4Å: Chain A: Y.672, V.697, L.700 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.672, A:Y.672, A:V.697, A:L.700 CLR.9: 7 residues within 4Å: Chain A: A.595, T.596, L.599, L.600, Y.659 Ligands: CLR.6, CLR.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.596, A:L.599, A:L.599, A:L.600, A:Y.659 CLR.12: 5 residues within 4Å: Chain B: W.576, I.600, Y.663, L.666 Ligands: CLR.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.576, B:I.600, B:Y.663, B:L.666, B:L.666 CLR.13: 4 residues within 4Å: Chain A: W.569 Chain B: L.669, W.676 Ligands: CLR.9 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.669, B:W.676, B:W.676, B:W.676, A:W.569 CLR.14: 4 residues within 4Å: Chain B: Y.691, I.734, C.737, I.745 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.734, B:I.745 CLR.15: 2 residues within 4Å: Chain B: M.495, L.744 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.744 CLR.16: 5 residues within 4Å: Chain B: M.694, N.698, I.701, M.702 Ligands: CLR.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.701 CLR.17: 6 residues within 4Å: Chain B: L.669, W.676, Y.697, I.701, I.704 Ligands: CLR.16 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.669, B:Y.697, B:I.701, B:I.704

1 x U3D: [(2R)-3-[(Z)-icos-11-enoyl]oxy-2-[(Z)-octadec-9-enoyl]oxypropyl] 2-(trimethylazaniumyl)ethyl phosphate(Non-covalent)

U3D.11: 27 residues within 4Å: Chain B: I.477, I.523, G.527, F.537, D.540, C.553, R.556, T.557, T.561, Y.564, A.567, E.646, H.647, C.648, V.660, Y.661, K.664, C.703, I.704, A.707, S.710, R.714, Q.720, V.724, I.728, S.732, T.735 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.523, B:Y.564, B:A.567, B:V.660, B:K.664, B:K.664, B:I.704, B:A.707, B:V.724 Hydrogen bonds: B:R.556, B:Q.720 Salt bridges: B:R.556, B:H.647, B:R.714

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., Structure of human GABABreceptor in an inactive state. Nature (2020)

Release Date

2020-07-01

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