SMTL ID : 8oqa.1

CryoEM structure of human rho1 GABAA receptor in complex with GABA and picrotoxin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.140 No protein-ligand interaction detected (PLIP) NAG.2: 1 residues within 4Å: Chain A: N.234 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain B: T.138, N.139, N.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.138 NAG.13: 1 residues within 4Å: Chain B: N.234 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain C: N.140, D.183 No protein-ligand interaction detected (PLIP) NAG.22: 3 residues within 4Å: Chain C: N.234, H.254, T.255 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.234, C:T.255 NAG.27: 1 residues within 4Å: Chain D: N.140 No protein-ligand interaction detected (PLIP) NAG.28: 1 residues within 4Å: Chain D: N.234 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:N.234 NAG.34: 1 residues within 4Å: Chain E: N.140 No protein-ligand interaction detected (PLIP) NAG.35: 1 residues within 4Å: Chain E: N.234 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.234

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

HEX.3: 3 residues within 4Å: Chain A: W.304 Chain E: Y.367 Ligands: HEX.4 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:Y.367, A:W.304 HEX.4: 3 residues within 4Å: Chain A: W.304 Chain E: Y.367 Ligands: HEX.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.304 HEX.5: 3 residues within 4Å: Chain A: W.475, S.479 Ligands: OCT.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.475 HEX.7: 2 residues within 4Å: Chain A: A.364 Chain B: W.304 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.304, A:A.364 HEX.14: 3 residues within 4Å: Chain B: A.364, Y.367 Chain C: W.304 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.364, B:Y.367, C:W.304 HEX.15: 2 residues within 4Å: Chain B: W.304, R.460 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.304 HEX.16: 2 residues within 4Å: Chain B: W.475 Ligands: OCT.17 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.475, B:W.475 HEX.18: 3 residues within 4Å: Chain B: I.341 Chain C: F.282 Ligands: OCT.23 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.282, C:F.282, B:I.341 HEX.24: 3 residues within 4Å: Chain C: A.364, Y.367 Chain D: W.304 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:A.364, C:Y.367, D:W.304 HEX.25: 5 residues within 4Å: Chain C: I.341, W.349 Chain D: L.286, F.290 Ligands: OCT.30 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.286, D:F.290, C:I.341, C:W.349 HEX.29: 3 residues within 4Å: Chain D: W.475, S.479 Ligands: OCT.30 No protein-ligand interaction detected (PLIP) HEX.31: 3 residues within 4Å: Chain D: A.364, Y.367 Chain E: W.304 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:A.364, D:Y.367, E:W.304 HEX.32: 1 residues within 4Å: Chain E: I.341 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.341 HEX.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x OCT: N-OCTANE(Non-covalent)

OCT.6: 4 residues within 4Å: Chain A: L.286, Y.347, W.475 Ligands: HEX.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.286 OCT.17: 6 residues within 4Å: Chain B: L.285, L.286, F.290, T.293, Y.347 Ligands: HEX.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.286 OCT.23: 3 residues within 4Å: Chain C: L.285, Y.347 Ligands: HEX.18 No protein-ligand interaction detected (PLIP) OCT.30: 5 residues within 4Å: Chain D: F.290, Y.347, W.475 Ligands: HEX.25, HEX.29 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.290

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 1 residues within 4Å: Ligands: CL.9 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Ligands: CL.8 Ligand excluded by PLIP

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

ABU.10: 8 residues within 4Å: Chain A: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain B: R.125, S.189 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.189, A:S.218 Salt bridges: B:R.125 Hydrophobic interactions: A:Y.262 ABU.11: 10 residues within 4Å: Chain B: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain C: Y.123, R.125, S.189 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.189, B:S.218 Salt bridges: C:R.125 Hydrophobic interactions: B:Y.262 ABU.20: 9 residues within 4Å: Chain C: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain D: Y.123, R.125, S.189 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.189, C:S.218 Salt bridges: D:R.125 Hydrophobic interactions: C:Y.262 ABU.26: 9 residues within 4Å: Chain D: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain E: R.125, S.189 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:S.189, D:S.218 Salt bridges: E:R.125 Hydrophobic interactions: D:Y.262 ABU.33: 10 residues within 4Å: Chain A: Y.123, R.125, S.189 Chain E: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.218, E:T.265, A:S.189 Salt bridges: A:R.125

1 x RI5: (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione(Non-covalent)

RI5.19: 13 residues within 4Å: Chain A: P.315, T.319 Chain B: P.315, T.319, L.322 Chain C: P.315, T.319, L.322 Chain D: P.315, T.319 Chain E: P.315, T.319, L.322 7 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C, 2 interactions with chain B, 1 interactions with chain E Hydrogen bonds: D:T.319, C:T.319 Hydrophobic interactions: C:P.315, C:T.319, B:T.319, B:L.322, E:L.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cowgill, J. et al., Structure and dynamics of differential ligand binding in the human rho-type GABA A receptor. Neuron (2023)

Release Date

2023-08-30

Peptides

Gamma-aminobutyric acid receptor subunit rho-1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

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

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