SMTL ID : 6d6u.1

Human GABA-A receptor alpha1-beta2-gamma2 subtype in complex with GABA and flumazenil, conformation A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.92 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: 5 residues within 4Å: Chain C: N.149, K.192, I.194, S.211, K.213 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.192, C:K.192, C:K.196

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[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.2: 7 residues within 4Å: Chain B: N.111 Chain E: S.137, N.138, G.141, D.157, W.160 Ligands: NAG-NAG-BMA-MAN-MAN.4 No protein-ligand interaction detected (PLIP)

1 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.4: 7 residues within 4Å: Chain B: S.92 Chain C: D.89, Q.90 Chain D: L.89, N.111, P.115 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.89 Hydrogen bonds: C:D.89, C:Q.90

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

NAG.5: 2 residues within 4Å: Chain A: N.80, H.119 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain C: P.78, 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.6: 7 residues within 4Å: Chain A: Y.157, F.200, T.202, Y.205 Chain B: F.65, R.67, T.130 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.65, A:Y.157, A:Y.205 Hydrogen bonds: B:T.130 Salt bridges: B:R.67 ABU.11: 7 residues within 4Å: Chain C: Y.97, Y.157, F.200, T.202, Y.205 Chain D: F.65, R.67 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.157, C:Y.205, D:F.65, D:F.65 Hydrogen bonds: C:Y.97, C:Y.97 Salt bridges: D:R.67

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 4 residues within 4Å: Chain A: L.235 Chain E: F.375, A.379 Ligands: Y01.21 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:F.375, E:A.379, A:L.235 Y01.8: 3 residues within 4Å: Chain B: L.301, N.308 Chain C: L.235 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.301, C:L.235 Y01.9: 7 residues within 4Å: Chain B: Y.294, F.298 Chain C: L.223, Q.224, M.227, L.231 Ligands: Y01.13 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:M.227, C:L.231, B:Y.294, B:F.298 Y01.12: 5 residues within 4Å: Chain C: M.294, S.320, F.323, F.324, V.327 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.323, C:F.324, C:F.324, C:V.327 Y01.13: 5 residues within 4Å: Chain B: V.263, T.267 Chain C: P.228 Chain E: L.311 Ligands: Y01.9 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: B:V.263, B:T.267, E:L.311, C:P.228 Y01.14: 5 residues within 4Å: Chain C: M.283, F.331, Y.338, Y.339 Ligands: Y01.16 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.331, C:F.331, C:Y.338, C:Y.339 Hydrogen bonds: C:Y.339 Y01.15: 1 residues within 4Å: Chain C: W.241 No protein-ligand interaction detected (PLIP) Y01.16: 4 residues within 4Å: Chain D: V.227, I.228, L.232 Ligands: Y01.14 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.227, D:L.232 Y01.17: 5 residues within 4Å: Chain D: I.223, V.227, I.235, W.341, L.345 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.227, D:V.227, D:W.341, D:W.341 Y01.18: 3 residues within 4Å: Chain D: L.324, F.329, L.332 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.329, D:L.332 Y01.19: 2 residues within 4Å: Chain D: L.301, N.308 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.301 Hydrogen bonds: D:N.308 Y01.21: 7 residues within 4Å: Chain A: L.235, L.253 Chain E: F.343, S.346, E.350, M.368 Ligands: Y01.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:L.235, A:L.253, E:F.343

1 x FYP: ethyl 8-fluoro-5-methyl-6-oxo-5,6-dihydro-4H-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate(Non-covalent)

FYP.20: 10 residues within 4Å: Chain D: H.102, Y.160, S.205, S.206, Y.210 Chain E: D.93, Y.95, F.114, A.116, T.179 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:Y.210, D:Y.210, E:Y.95 pi-Stacking: E:F.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, S. et al., Structure of a human synaptic GABAAreceptor. Nature (2018)

Release Date

2018-06-27

Peptides

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

Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit gamma-2,Gamma-aminobutyric acid receptor subunit gamma-2

Kappa Fab Light Chain

IgG2b Fab Heavy Chain

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