SMTL ID : 6x3t.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.55 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: 7 residues within 4Å: Chain A: N.149, D.190, K.192, I.194, K.196, S.211, K.213 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 7 residues within 4Å: Chain C: N.149, D.190, K.192, I.194, K.196, S.211, K.213 No protein-ligand interaction detected (PLIP) 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: 16 residues within 4Å: 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, D.157, W.160, P.164 Ligands: NAG-NAG-BMA.4 No protein-ligand interaction detected (PLIP)

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: 5 residues within 4Å: Chain E: W.220, K.221, R.222, S.224, N.245 No protein-ligand interaction detected (PLIP)

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.9: 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: 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 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:T.130, A:Y.157 Salt bridges: B:R.67 Hydrogen bonds: A:Y.97, A:E.155, A:T.202, A:T.202 ABU.10: 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: 3 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.118, C:Y.157, C:Y.205 Hydrogen bonds: D:T.130, C:Y.97, C:Y.157, C:Y.157 Salt bridges: D:R.67

2 x PFL: 2,6-BIS(1-METHYLETHYL)PHENOL(Non-covalent)

PFL.8: 10 residues within 4Å: Chain A: N.265, D.282, L.285, M.286, F.289 Chain B: I.228, Q.229, L.232, P.233, M.236 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.289, A:F.289 Hydrogen bonds: B:I.228 PFL.11: 10 residues within 4Å: Chain C: N.265, D.282, L.285, M.286, F.289 Chain D: I.228, Q.229, L.232, P.233, M.236 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:M.236, C:N.265, C:D.282, C:F.289, C:F.289 Hydrogen bonds: D:I.228

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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