SMTL ID : 6x40.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.86 Å

Oligo State

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

Ligands

3 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 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 6 residues within 4Å: Chain C: N.149, K.192, I.194, K.196, S.211, K.213 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.196 NAG-NAG-BMA.4: 6 residues within 4Å: Chain C: D.89 Chain D: N.111, M.114, P.115 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: 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.2: 19 residues within 4Å: Chain A: G.108, K.112 Chain B: N.111, T.113 Chain D: N.28, S.92, N.111, P.115, K.117 Chain E: S.137, N.138, V.140, G.141, K.142, K.155, D.157, W.160, P.164 Ligands: NAG-NAG-BMA.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.112, A:G.108

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 No protein-ligand interaction detected (PLIP)

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

NAG.6: 4 residues within 4Å: Chain A: P.78, L.79, N.80, H.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 NAG.8: 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

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

ABU.7: 11 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, L.118, T.130 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.200, A:Y.205, B:F.65, B:L.118 Hydrogen bonds: A:S.156, A:T.202 Salt bridges: B:R.67 ABU.9: 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 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.65, D:L.118, C:F.200, C:Y.205 Salt bridges: D:R.67 Hydrogen bonds: C:Y.97, C:S.156

1 x RI5: (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione(Non-covalent)

RI5.10: 12 residues within 4Å: Chain A: A.252, T.256 Chain B: V.257, T.261 Chain C: A.252, I.255, T.256 Chain D: V.257, T.261 Chain E: S.304, T.308, L.311 7 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:I.255, C:T.256, D:V.257, D:V.257, A:A.252, B:V.257 Hydrogen bonds: D:T.261

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 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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