SMTL ID : 6x3z.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.23 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 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain C: N.149, K.192, I.194, S.211, K.213 No protein-ligand interaction detected (PLIP)

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: 20 residues within 4Å: Chain A: G.108, K.112 Chain B: N.111, T.113 Chain D: N.28, S.92, 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, R.166 Ligands: NAG.9 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.4: 5 residues within 4Å: Chain E: R.222, S.224, L.243, R.244, N.245 No protein-ligand interaction detected (PLIP)

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

NAG.5: 4 residues within 4Å: Chain A: P.78, L.79, N.80, H.119 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.79 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: 6 residues within 4Å: 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, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.111

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

ABU.6: 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: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.65, B:L.118, A:F.200, A:Y.205 Salt bridges: B:R.67 Hydrogen bonds: A:S.156, A:T.202 ABU.8: 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 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.200, C:Y.205, D:F.65, D:L.118 Hydrogen bonds: C:Y.97, C:S.156, D:T.130, D:T.130 Salt bridges: D:R.67

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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