SMTL ID : 7pbz.1

a1b3 GABA-A receptor + GABA + Zn2+

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-1-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain C: N.80, H.119 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain D: P.78, N.80, H.119 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain E: P.78, L.79, N.80, H.119 No protein-ligand interaction detected (PLIP)

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.2: 7 residues within 4Å: Chain C: N.149, R.192, V.194, S.195, R.196, S.211, R.213 No protein-ligand interaction detected (PLIP)

2 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: 12 residues within 4Å: Chain A: N.417, Y.418, S.490, T.497, D.500 Chain D: N.149, R.192, V.194, S.195, R.196, S.211, R.213 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.418, A:D.500, A:D.500, D:R.192, D:R.192, D:R.196, D:R.196 NAG-NAG-BMA-MAN-MAN.6: 8 residues within 4Å: Chain E: N.149, E.190, R.192, V.194, S.195, R.196, S.211, R.213 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.192

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

NAG.7: 3 residues within 4Å: Chain B: N.110, T.112, P.114 No protein-ligand interaction detected (PLIP) NAG.19: 3 residues within 4Å: Chain F: N.164, M.167, P.168 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.164

2 x UND: UNDECANE(Non-covalent)

UND.8: 5 residues within 4Å: Chain B: S.298, S.324, F.328, L.331 Ligands: OCT.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.328, B:F.328, B:L.331 UND.10: 6 residues within 4Å: Chain B: I.301, T.305, Y.308, F.309 Chain E: V.238, W.241 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: E:V.238, E:W.241, E:W.241, E:W.241, B:I.301, B:Y.308, B:F.309

2 x OCT: N-OCTANE(Non-covalent)(Non-functional Binders)

OCT.9: 3 residues within 4Å: Chain B: S.298, I.301 Ligands: UND.8 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.301 OCT.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x HEX: HEXANE(Non-covalent)(Non-functional Binders)

HEX.12: 5 residues within 4Å: Chain B: A.290, Y.293 Chain E: L.223, M.227, L.231 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.231 HEX.14: 3 residues within 4Å: Chain C: W.237, F.438, N.442 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.237, C:F.438 HEX.20: 1 residues within 4Å: Chain F: W.394 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:W.394, F:W.394 HEX.21: 1 residues within 4Å: Ligands: D10.22 No protein-ligand interaction detected (PLIP)

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

ABU.13: 10 residues within 4Å: Chain B: F.64, R.66, T.129 Chain C: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.200, C:Y.205, B:F.64 Hydrogen bonds: C:Y.97, C:E.155, C:Y.157 Salt bridges: B:R.66 ABU.18: 11 residues within 4Å: Chain E: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 Chain F: F.118, R.120, L.171, T.183 9 PLIP interactions: 3 interactions with chain F, 6 interactions with chain E Hydrophobic interactions: F:F.118, F:L.171, E:Y.157, E:Y.205 Salt bridges: F:R.120 Hydrogen bonds: E:Y.97, E:E.155, E:Y.157, E:T.202

1 x ZN: ZINC ION(Non-covalent)

ZN.15: 3 residues within 4Å: Chain C: H.267 Chain D: H.267 Chain E: H.267 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 1 interactions with chain C Metal complexes: D:H.267, E:H.267, C:H.267

1 x HSM: HISTAMINE(Non-covalent)

HSM.16: 5 residues within 4Å: Chain D: Y.97, E.155, S.156, Y.157, T.202 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.97, D:Y.97, D:T.202

3 x D10: DECANE(Non-covalent)

D10.17: 5 residues within 4Å: Chain D: V.238, W.241 Chain F: T.359, F.363 Ligands: D10.22 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: F:T.359, F:F.363, D:V.238, D:W.241, D:W.241, D:W.241 D10.22: 5 residues within 4Å: Chain F: E.356, T.359 Ligands: D10.17, HEX.21, D10.23 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:E.356 D10.23: 5 residues within 4Å: Chain F: I.374, L.377, F.382, L.385 Ligands: D10.22 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:I.374, F:L.377, F:F.382, F:F.382, F:L.385

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
A

C
B

D
C

E
E

F
D

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

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