SMTL ID : 6x3s.1

Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with bicuculline methbromide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.12 Å

Oligo State

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

Ligands

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.1: 6 residues within 4Å: Chain A: N.149, 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.3: 7 residues within 4Å: Chain C: N.149, D.190, K.192, I.194, K.196, S.211, K.213 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: 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-(1-2)-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.2: 17 residues within 4Å: Chain A: K.112 Chain B: N.111, T.113 Chain D: A.109, N.111, P.115, K.117 Chain E: S.137, N.138, V.140, G.141, K.142, D.157, W.160, P.164 Ligands: NAG.9, MAN.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:K.112, D:A.109, D:K.117

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.4: 6 residues within 4Å: Chain E: W.220, K.221, R.222, L.243, R.244, N.245 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:R.222

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

NAG.5: 2 residues within 4Å: Chain A: N.80, H.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 NAG.7: 4 residues within 4Å: Chain C: P.78, L.79, N.80, H.119 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.80 NAG.9: 5 residues within 4Å: Chain D: N.111, P.115 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.111

2 x J94: (5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-6-ium(Non-covalent)

J94.6: 9 residues within 4Å: Chain A: E.155, Y.157, F.200, T.202, Y.205 Chain B: F.46, F.65, R.67, T.130 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.65, B:T.130 Hydrogen bonds: B:R.67 pi-Stacking: A:F.200 pi-Cation interactions: A:Y.157 J94.8: 10 residues within 4Å: Chain C: Y.97, S.156, Y.157, F.200, T.202, Y.205 Chain D: F.46, F.65, R.67, T.130 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.65, D:T.130 Hydrogen bonds: D:R.67 pi-Stacking: C:F.200 pi-Cation interactions: C:Y.157

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.10: 4 residues within 4Å: Chain E: K.155, D.157 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.155, E:K.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J.J. et al., Shared structural mechanisms of general anaesthetics and benzodiazepines. Nature (2020)

Release Date

2020-09-09

Peptides

Gamma-aminobutyric acid receptor subunit beta-2: AC
Gamma-aminobutyric acid receptor subunit alpha-1: BD
Gamma-aminobutyric acid type A 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 type A receptor subunit gamma-2

Kappa Fab Light Chain

IgG2b Fab Heavy Chain

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