SMTL ID : 8vrn.1

Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus PPTQ

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-2-2-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain C: L.79, N.80, H.119 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain E: W.220, K.221, R.222, L.243, R.244, N.245 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: P.78, N.80, H.119 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 7 residues within 4Å: Chain A: N.149, D.190, K.192, I.194, K.196, S.211, K.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.196 NAG-NAG-BMA-MAN-MAN.4: 6 residues within 4Å: Chain C: N.149, D.190, K.192, K.196, S.211, K.213 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.192, C:K.196 NAG-NAG-BMA-MAN-MAN.7: 8 residues within 4Å: Chain B: S.92 Chain C: D.89 Chain D: N.111, M.114, P.115 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.3 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.89, C:D.89

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.3: 17 residues within 4Å: Chain A: R.86 Chain B: N.111, T.113 Chain D: N.28, A.109, N.111, P.115, K.117 Chain E: S.137, N.138, V.140, G.141, K.142, A.156, D.157, W.160 Ligands: NAG-NAG-BMA-MAN-MAN.7 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.157

2 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.8: 10 residues within 4Å: Chain A: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 Chain B: F.65, R.67, T.130 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.157, A:Y.205 Hydrogen bonds: A:Y.97, A:E.155 Salt bridges: B:R.67 ABU.13: 11 residues within 4Å: Chain C: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 Chain D: F.65, R.67, L.118, T.130 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.65, D:L.118 Hydrogen bonds: D:T.130, C:S.156, C:T.202 Salt bridges: D:R.67

2 x 01: 3-(4-methylphenyl)-2-phenylquinazolin-4(3H)-one

01.9: 12 residues within 4Å: Chain A: T.262, N.265, D.282, L.285, M.286, F.289 Chain B: I.228, L.232, P.233, M.236, T.237, T.265 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.228, B:L.232, B:P.233, B:T.265, A:T.262, A:D.282, A:L.285, A:F.289, A:F.289 Hydrogen bonds: A:N.265 01.14: 13 residues within 4Å: Chain C: T.262, N.265, D.282, M.286, F.289 Chain D: I.228, L.232, P.233, M.236, T.237, T.265, L.269 Ligands: PTY.19 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:I.228, D:L.232, D:P.233, D:M.236, D:T.265, D:L.269, C:T.262, C:N.265, C:M.286, C:F.289, C:F.289 Hydrogen bonds: C:N.265

5 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.10: 13 residues within 4Å: Chain A: Y.277, V.278, M.283, M.286, G.287, F.291, F.330, F.331, V.334, Y.338, Y.339 Ligands: PTY.11, POV.12 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.291, A:F.291, A:F.330, A:F.331, A:V.334, A:Y.338, A:Y.338 Hydrogen bonds: A:V.278 PTY.11: 11 residues within 4Å: Chain B: K.222, I.223, G.224, V.227, I.228, L.232, I.235, N.337, W.341 Ligands: PTY.10, POV.12 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.227, B:V.227, B:I.228, B:L.232, B:I.235, B:N.337, B:W.341 Hydrogen bonds: B:I.223, B:G.224 PTY.15: 7 residues within 4Å: Chain C: L.297, L.301, Y.304 Chain D: V.243, W.246, R.326, I.327 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.243, D:W.246, D:W.246, D:I.327, D:I.327, C:L.301, C:Y.304 PTY.17: 11 residues within 4Å: Chain C: Y.277, V.278, M.283, M.286, G.287, F.291, F.330, F.331, V.334, Y.338 Ligands: PTY.19 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.330, C:F.331, C:V.334, C:Y.338 Hydrogen bonds: C:V.278 PTY.19: 13 residues within 4Å: Chain C: P.276 Chain D: K.222, I.223, G.224, V.227, I.228, L.232, I.235, F.333, N.337, W.341 Ligands: 01.14, PTY.17 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.227, D:I.228, D:L.232, D:I.235, D:F.333, D:N.337, D:W.341 Hydrogen bonds: D:I.223, D:G.224

1 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.12: 3 residues within 4Å: Chain B: L.232 Ligands: PTY.10, PTY.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.232

2 x Q3G: O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine(Non-covalent)

Q3G.16: 8 residues within 4Å: Chain B: I.302, T.306, Y.309, F.310 Chain C: V.238, W.241, I.322, S.329 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:I.302, B:Y.309, C:V.238, C:W.241, C:W.241, C:W.241, C:W.241, C:I.322 Hydrogen bonds: B:Y.309 Q3G.18: 11 residues within 4Å: Chain D: A.295, F.296, F.298, S.299, T.306, R.317, K.320, I.321, S.325, F.329, L.332 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:A.295, D:F.296, D:F.296, D:F.298, D:I.321, D:F.329, D:L.332 Hydrogen bonds: D:T.306 Salt bridges: D:R.317, D:R.317

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chojnacka, W. et al., Structural insights into GABA A receptor potentiation by Quaalude. Nat Commun (2024)

Release Date

2024-06-26

Peptides

Gamma-aminobutyric acid receptor subunit beta-2: AC
Gamma-aminobutyric acid receptor subunit alpha-1: BD
Gamma-aminobutyric acid receptor subunit gamma-2: E
Kappa FAB light chain: FH
IGG2B FAB heavy chain: GI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
I

H
L

G
J

I
K

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit beta-2

Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit gamma-2

Kappa FAB light chain

IGG2B FAB heavy chain

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