SMTL ID : 9drx.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.1: 5 residues within 4Å: Chain C: D.89 Chain D: N.111, T.113, M.114 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.3 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: N.149, K.192, I.194, K.196, S.211, K.213 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 7 residues within 4Å: Chain C: N.149, D.190, K.192, I.194, K.196, S.211, K.213 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.196, C:K.196

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.3: 12 residues within 4Å: Chain A: K.112 Chain B: N.111, T.113 Chain D: N.28, S.92 Chain E: S.137, N.138, V.140, G.141, K.142, W.160 Ligands: NAG-NAG-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.112

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

NAG-NAG.5: 7 residues within 4Å: Chain E: W.220, K.221, R.222, S.224, L.243, R.244, N.245 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.222

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

NAG.6: 2 residues within 4Å: Chain A: N.80, H.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 NAG.8: 1 residues within 4Å: Chain C: N.80 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.80

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

ABU.7: 8 residues within 4Å: Chain A: Y.97, E.155, S.156, Y.157, T.202, Y.205 Chain B: R.67, T.130 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.157, A:Y.205 Hydrogen bonds: A:S.156, A:T.202, A:Y.205, A:Y.205, B:T.130 Salt bridges: B:R.67 ABU.9: 10 residues within 4Å: Chain C: Y.97, E.155, S.156, Y.157, T.202, Y.205 Chain D: F.65, R.67, L.118, T.130 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.65, D:F.65, D:T.130, C:Y.157 Hydrogen bonds: D:T.130, C:S.156, C:Y.205 Salt bridges: D:R.67

1 x IYJ: (6M)-6-(2,3-dichlorophenyl)-1,2,4-triazine-3,5-diamine(Non-covalent)

IYJ.10: 7 residues within 4Å: Chain D: H.102, V.203, Q.204, S.205, Y.210 Chain E: Y.95, E.226 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Salt bridges: E:E.226 pi-Stacking: E:Y.95, D:H.102 pi-Cation interactions: E:Y.95 Hydrophobic interactions: D:V.203, D:Y.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, J. et al., Resolving native GABA A receptor structures from the human brain. Nature (2025)

Release Date

2025-01-22

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 1F4 Light Chain: FH
IgG2b Fab 1F4 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 1F4 Light Chain

IgG2b Fab 1F4 Heavy Chain

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