SMTL ID : 8g4o.1

Native GABA-A receptor from the mouse brain, alpha1-beta2-gamma2 subtype, in complex with didesethylflurazepam and endogenous GABA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.1: 14 residues within 4Å: Chain A: N.137, T.139 Chain D: S.138, N.139, V.141, G.142, K.143, A.157, D.158, W.161, P.165, R.167 Chain E: K.136 Ligands: NAG-NAG-BMA-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.157

5 x NAG- NAG- BMA- MAN- MAN: 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.2: 4 residues within 4Å: Chain B: P.102, L.103, N.104, H.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 7 residues within 4Å: Chain B: N.173, K.216, I.218, K.220, S.233, S.235, K.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.220 NAG-NAG-BMA-MAN-MAN.4: 3 residues within 4Å: Chain B: D.113 Chain C: N.137 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.113 NAG-NAG-BMA-MAN-MAN.6: 2 residues within 4Å: Chain E: N.104, H.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.7: 6 residues within 4Å: Chain E: N.173, K.216, I.218, K.220, S.235, K.237 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.216, E:K.220

1 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.5: 5 residues within 4Å: Chain D: W.221, R.223, S.225, L.244, N.246 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.223

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

ABU.8: 6 residues within 4Å: Chain A: F.91, R.93, T.156 Chain E: Y.121, Y.181, F.224 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.91 Salt bridges: A:R.93 ABU.9: 7 residues within 4Å: Chain B: E.179, Y.181, Y.229 Chain C: F.91, R.93, L.144, T.156 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.179 Salt bridges: C:R.93

1 x YNL: (5M)-1-(2-aminoethyl)-7-chloro-5-(2-fluorophenyl)-1,3-dihydro-2H-1,4-benzodiazepin-2-one(Non-covalent)

YNL.10: 11 residues within 4Å: Chain C: H.128, S.185, Y.186, V.229, Q.230, S.231, S.232, Y.236 Chain D: Y.96, N.98, F.115 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.236, D:Y.96, D:F.115 Hydrogen bonds: C:S.231, C:S.232 pi-Stacking: C:Y.236 Halogen bonds: C:H.128

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

NAG.11: 2 residues within 4Å: Chain D: K.126, N.128 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, C. et al., Cryo-EM structures reveal native GABA A receptor assemblies and pharmacology. Nature (2023)

Release Date

2023-09-20

Peptides

Gamma-aminobutyric acid receptor subunit alpha-1: AC
Gamma-aminobutyric acid receptor subunit beta-2: BE
Gamma-aminobutyric acid receptor subunit gamma-2: D
Heavy Chain of 8E3 Fab: FG
Light Chain of 8E3 Fab: HI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

E
E

D
D

F
H

G
J

H
K

I
L

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit beta-2

Gamma-aminobutyric acid receptor subunit gamma-2

Heavy Chain of 8E3 Fab

Light Chain of 8E3 Fab

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