SMTL ID : 7pc0.1

GABA-A receptor bound by a-Cobratoxin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-1-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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: 13 residues within 4Å: Chain C: N.149, E.190, R.192, V.194, S.195, R.196, S.209, S.211, R.213 Chain G: T.6, P.7, D.38, L.39 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.209

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.2: 3 residues within 4Å: Chain C: P.78, N.80, H.119 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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.3: 11 residues within 4Å: Chain A: N.417, Y.418, S.490, D.500 Chain D: N.149, R.192, V.194, S.195, R.196, S.211, R.213 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.196, A:Y.418

1 x NAG- NAG- BMA- MAN: 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.4: 13 residues within 4Å: Chain E: N.149, E.190, R.192, V.194, S.195, R.196, N.197, S.211, F.212, R.213 Chain H: T.6, P.7, D.8 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:S.195, E:N.197, H:T.6, H:D.8, E:R.192

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

NAG.5: 2 residues within 4Å: Chain B: N.110, P.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.110 NAG.8: 1 residues within 4Å: Chain D: N.80 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.80 NAG.9: 2 residues within 4Å: Chain E: N.80, H.119 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.119 NAG.10: 1 residues within 4Å: Chain F: N.164 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.164

1 x HSM: HISTAMINE(Non-covalent)

HSM.6: 4 residues within 4Å: Chain C: D.43, Y.62 Chain D: T.202, Y.205 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.157 Hydrophobic interactions: C:Y.62

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain C: H.267 Chain D: H.267 Chain E: H.267 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C, 1 interactions with chain D Metal complexes: E:H.267, C:H.267, D:H.267

1 x HEX: HEXANE(Non-covalent)

HEX.11: 1 residues within 4Å: Chain F: V.280 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., Mechanisms of inhibition and activation of extrasynaptic alpha beta GABA A receptors. Nature (2022)

Release Date

2022-02-09

Peptides

Megabody 25: A
Gamma-aminobutyric acid receptor subunit alpha-1: B
Gamma-aminobutyric acid receptor subunit beta-3: CDE
Gamma-aminobutyric acid receptor subunit alpha-1: F
Alpha-cobratoxin: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
A

C
B

D
C

E
E

F
D

G
K

H
L

Membrane

We predict this structure to be a membrane protein.
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Megabody 25

Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit beta-3

Gamma-aminobutyric acid receptor subunit alpha-1

Alpha-cobratoxin

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