SMTL ID : 9frg.1

CryoEM structure of human rho1 GABAA receptor in complex with (S)-GABOB in the desensitized state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 1 residues within 4Å: Chain A: N.140 No protein-ligand interaction detected (PLIP) NAG.2: 3 residues within 4Å: Chain A: N.234, H.254, T.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.234, A:H.254 NAG.11: 1 residues within 4Å: Chain B: N.140 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain B: N.234, H.254, T.255 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.234, B:H.254 NAG.20: 1 residues within 4Å: Chain C: N.140 No protein-ligand interaction detected (PLIP) NAG.21: 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:H.254 NAG.28: 1 residues within 4Å: Chain D: N.140 No protein-ligand interaction detected (PLIP) NAG.29: 3 residues within 4Å: Chain D: N.234, H.254, T.255 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.234, D:H.254 NAG.36: 1 residues within 4Å: Chain E: N.140 No protein-ligand interaction detected (PLIP) NAG.37: 3 residues within 4Å: Chain E: N.234, H.254, T.255 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.234, E:H.254

5 x D10: DECANE(Non-covalent)

D10.3: 4 residues within 4Å: Chain A: M.297, W.304 Chain B: A.364, Y.367 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.364, B:Y.367, A:W.304 D10.13: 4 residues within 4Å: Chain B: M.297, W.304 Chain E: A.364, Y.367 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:Y.367, B:W.304 D10.22: 4 residues within 4Å: Chain A: A.364, Y.367 Chain C: M.297, W.304 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.367, C:W.304 D10.30: 4 residues within 4Å: Chain C: A.364, Y.367 Chain D: M.297, 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 D10.38: 4 residues within 4Å: Chain D: A.364, Y.367 Chain E: M.297, 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

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

OCT.4: 5 residues within 4Å: Chain A: L.285, F.290, T.293, W.475 Ligands: HEX.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.285, A:F.290, A:F.290, A:W.475 OCT.6: 4 residues within 4Å: Chain A: F.470, I.473, I.477 Ligands: HEX.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.470, A:I.473 OCT.14: 5 residues within 4Å: Chain B: L.285, F.290, T.293, W.475 Ligands: HEX.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.285, B:F.290, B:F.290, B:W.475 OCT.16: 4 residues within 4Å: Chain B: F.470, I.473, I.477 Ligands: HEX.17 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.470, B:I.473 OCT.23: 5 residues within 4Å: Chain C: L.285, F.290, T.293, W.475 Ligands: HEX.24 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.285, C:F.290, C:F.290, C:W.475 OCT.25: 4 residues within 4Å: Chain C: F.470, I.473, I.477 Ligands: HEX.26 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.470, C:I.473 OCT.31: 5 residues within 4Å: Chain D: L.285, F.290, T.293, W.475 Ligands: HEX.32 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.285, D:F.290, D:F.290, D:W.475 OCT.33: 4 residues within 4Å: Chain D: F.470, I.473, I.477 Ligands: HEX.34 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.470, D:I.473 OCT.39: 5 residues within 4Å: Chain E: L.285, F.290, T.293, W.475 Ligands: HEX.40 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.285, E:F.290, E:F.290, E:W.475 OCT.41: 4 residues within 4Å: Chain E: F.470, I.473, I.477 Ligands: HEX.42 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.470, E:I.473

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

HEX.5: 2 residues within 4Å: Chain A: W.475 Ligands: OCT.4 No protein-ligand interaction detected (PLIP) HEX.7: 1 residues within 4Å: Ligands: OCT.6 No protein-ligand interaction detected (PLIP) HEX.15: 2 residues within 4Å: Chain B: W.475 Ligands: OCT.14 No protein-ligand interaction detected (PLIP) HEX.17: 1 residues within 4Å: Ligands: OCT.16 No protein-ligand interaction detected (PLIP) HEX.24: 2 residues within 4Å: Chain C: W.475 Ligands: OCT.23 No protein-ligand interaction detected (PLIP) HEX.26: 1 residues within 4Å: Ligands: OCT.25 No protein-ligand interaction detected (PLIP) HEX.32: 2 residues within 4Å: Chain D: W.475 Ligands: OCT.31 No protein-ligand interaction detected (PLIP) HEX.34: 1 residues within 4Å: Ligands: OCT.33 No protein-ligand interaction detected (PLIP) HEX.40: 2 residues within 4Å: Chain E: W.475 Ligands: OCT.39 No protein-ligand interaction detected (PLIP) HEX.42: 1 residues within 4Å: Ligands: OCT.41 No protein-ligand interaction detected (PLIP)

5 x 01: (S)-amino-3-hydroxybutanoic acid

01.8: 10 residues within 4Å: Chain A: Y.123, R.125, M.177, S.189 Chain B: E.217, S.218, Y.219, Y.262, T.265, Y.268 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.217, B:Y.219, B:Y.219, B:T.265, B:T.265, B:Y.268, A:S.189 Hydrophobic interactions: A:Y.123 Salt bridges: A:R.125 01.18: 10 residues within 4Å: Chain B: Y.123, R.125, M.177, S.189 Chain E: E.217, S.218, Y.219, Y.262, T.265, Y.268 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain E Hydrophobic interactions: B:Y.123 Hydrogen bonds: B:S.189, E:E.217, E:Y.219, E:Y.219, E:T.265, E:T.265, E:Y.268 Salt bridges: B:R.125 01.19: 10 residues within 4Å: Chain A: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain C: Y.123, R.125, M.177, S.189 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:Y.123 Hydrogen bonds: C:S.189, A:E.217, A:Y.219, A:Y.219, A:T.265, A:T.265, A:Y.268 Salt bridges: C:R.125 01.27: 10 residues within 4Å: Chain C: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain D: Y.123, R.125, M.177, S.189 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:Y.123 Hydrogen bonds: D:S.189, C:E.217, C:Y.219, C:Y.219, C:T.265, C:T.265, C:Y.268 Salt bridges: D:R.125 01.35: 10 residues within 4Å: Chain D: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain E: Y.123, R.125, M.177, S.189 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:Y.123 Hydrogen bonds: E:S.189, D:E.217, D:Y.219, D:Y.219, D:T.265, D:T.265, D:Y.268 Salt bridges: E:R.125

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

CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: P.311 Chain B: P.311 Chain C: P.311 Chain D: P.311 Chain E: P.311 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, C. et al., Cryo-EM structures of Rho1 GABAA receptors with antagonist and agonist drugs. To Be Published

Release Date

2025-07-02

Peptides

Gamma-aminobutyric acid receptor subunit rho-1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
B

D
C

E
D

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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