SMTL ID : 9frb.1

CryoEM structure of human rho1 GABAA receptor in complex with CGP36742

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x 01: 3-azanylpropyl(butyl)phosphinic acid

01.1: 10 residues within 4Å: Chain A: E.217, S.218, Y.219, Y.262, S.264, T.265, Y.268 Chain B: R.125, M.177, S.189 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:M.177, A:T.265 Hydrogen bonds: B:R.125, B:S.189, A:E.217 01.14: 11 residues within 4Å: Chain B: E.217, S.218, Y.219, Y.262, S.264, T.265, Y.268 Chain C: R.125, M.177, R.179, S.189 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:M.177, B:T.265 Hydrogen bonds: C:R.125, C:S.189, B:E.217 01.25: 11 residues within 4Å: Chain C: E.217, S.218, Y.219, Y.262, S.264, T.265, Y.268 Chain D: R.125, M.177, R.179, S.189 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:M.177, D:R.179, C:T.265 Hydrogen bonds: D:R.125, D:S.189, C:E.217 01.37: 11 residues within 4Å: Chain D: E.217, S.218, Y.219, Y.262, S.264, T.265, Y.268 Chain E: R.125, M.177, R.179, S.189 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:T.265, E:M.177, E:R.179 Hydrogen bonds: D:E.217, E:R.125, E:S.189, E:S.189 01.48: 11 residues within 4Å: Chain A: R.125, M.177, R.179, S.189 Chain E: E.217, S.218, Y.219, Y.262, S.264, T.265, Y.268 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:M.177, A:R.179, E:T.265 Hydrogen bonds: A:R.125, A:S.189, E:E.217

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

NAG.2: 3 residues within 4Å: Chain A: T.138, N.139, N.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.138 NAG.3: 4 residues within 4Å: Chain A: G.233, N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.255 NAG.15: 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.16: 4 residues within 4Å: Chain B: G.233, N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.255 NAG.26: 3 residues within 4Å: Chain C: T.138, N.139, N.140 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.138 NAG.27: 4 residues within 4Å: Chain C: G.233, N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.255 NAG.38: 3 residues within 4Å: Chain D: T.138, N.139, N.140 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.138 NAG.39: 4 residues within 4Å: Chain D: G.233, N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.255 NAG.49: 3 residues within 4Å: Chain E: T.138, N.139, N.140 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.138 NAG.50: 4 residues within 4Å: Chain E: G.233, N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.255

15 x HEX: HEXANE(Non-covalent)

HEX.4: 4 residues within 4Å: Chain A: Y.458, S.459, I.462 Ligands: HEX.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.458, A:I.462 HEX.5: 3 residues within 4Å: Chain A: L.357, E.361 Ligands: HEX.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.361 HEX.6: 2 residues within 4Å: Chain A: I.346, F.478 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.346, A:F.478 HEX.17: 4 residues within 4Å: Chain B: Y.458, S.459, I.462 Ligands: HEX.18 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.458, B:I.462 HEX.18: 3 residues within 4Å: Chain B: L.357, E.361 Ligands: HEX.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.361 HEX.19: 2 residues within 4Å: Chain B: I.346, F.478 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.346, B:F.478 HEX.28: 4 residues within 4Å: Chain C: Y.458, S.459, I.462 Ligands: HEX.29 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.458, C:I.462 HEX.29: 3 residues within 4Å: Chain C: L.357, E.361 Ligands: HEX.28 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.361 HEX.30: 2 residues within 4Å: Chain C: I.346, F.478 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.346, C:F.478 HEX.40: 4 residues within 4Å: Chain D: Y.458, S.459, I.462 Ligands: HEX.41 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.458, D:I.462 HEX.41: 3 residues within 4Å: Chain D: L.357, E.361 Ligands: HEX.40 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.361 HEX.42: 2 residues within 4Å: Chain D: I.346, F.478 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.346, D:F.478 HEX.51: 4 residues within 4Å: Chain E: Y.458, S.459, I.462 Ligands: HEX.52 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.458, E:I.462 HEX.52: 3 residues within 4Å: Chain E: L.357, E.361 Ligands: HEX.51 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:E.361 HEX.53: 2 residues within 4Å: Chain E: I.346, F.478 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.346, E:F.478

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

OCT.7: 3 residues within 4Å: Chain A: N.471, W.475 Ligands: D12.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.471, A:W.475 OCT.20: 3 residues within 4Å: Chain B: N.471, W.475 Ligands: D12.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.471, B:W.475 OCT.31: 3 residues within 4Å: Chain C: N.471, W.475 Ligands: D12.32 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.471, C:W.475 OCT.43: 3 residues within 4Å: Chain D: N.471, W.475 Ligands: D12.44 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.471, D:W.475 OCT.54: 3 residues within 4Å: Chain E: N.471, W.475 Ligands: D12.55 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:N.471, E:W.475

10 x D12: DODECANE(Non-covalent)

D12.8: 2 residues within 4Å: Chain A: W.475 Ligands: OCT.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.475, A:W.475, A:W.475 D12.10: 4 residues within 4Å: Chain A: I.341, W.349, V.353 Chain B: F.290 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.341, A:W.349, A:V.353, B:F.290 D12.21: 2 residues within 4Å: Chain B: W.475 Ligands: OCT.20 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.475, B:W.475, B:W.475 D12.23: 4 residues within 4Å: Chain B: I.341, W.349, V.353 Chain C: F.290 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.341, B:W.349, B:V.353, C:F.290 D12.32: 2 residues within 4Å: Chain C: W.475 Ligands: OCT.31 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.475, C:W.475, C:W.475 D12.34: 4 residues within 4Å: Chain C: I.341, W.349, V.353 Chain D: F.290 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.290, C:I.341, C:W.349, C:V.353 D12.44: 2 residues within 4Å: Chain D: W.475 Ligands: OCT.43 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.475, D:W.475, D:W.475 D12.46: 4 residues within 4Å: Chain D: I.341, W.349, V.353 Chain E: F.290 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:F.290, D:I.341, D:W.349, D:V.353 D12.55: 2 residues within 4Å: Chain E: W.475 Ligands: OCT.54 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:W.475, E:W.475, E:W.475 D12.57: 4 residues within 4Å: Chain A: F.290 Chain E: I.341, W.349, V.353 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:I.341, E:W.349, E:V.353, A:F.290

10 x D10: DECANE(Non-covalent)

D10.9: 3 residues within 4Å: Chain A: W.304, R.460, I.461 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.304 D10.11: 2 residues within 4Å: Chain A: W.304 Chain E: Y.367 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:W.304, E:Y.367 D10.13: 2 residues within 4Å: Chain A: Y.367 Chain B: W.304 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.304, A:Y.367 D10.22: 3 residues within 4Å: Chain B: W.304, R.460, I.461 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.304 D10.24: 2 residues within 4Å: Chain B: Y.367 Chain C: W.304 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.367, C:W.304 D10.33: 3 residues within 4Å: Chain C: W.304, R.460, I.461 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.304 D10.36: 4 residues within 4Å: Chain C: Y.367 Chain D: M.297, V.301, W.304 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.367, D:V.301, D:W.304, D:W.304 D10.45: 3 residues within 4Å: Chain D: W.304, R.460, I.461 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.304 D10.47: 2 residues within 4Å: Chain D: Y.367 Chain E: W.304 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:Y.367, E:W.304 D10.56: 3 residues within 4Å: Chain E: W.304, R.460, I.461 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.304

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

CL.12: 1 residues within 4Å: Ligands: CL.35 Ligand excluded by PLIP CL.35: 6 residues within 4Å: Chain A: P.311 Chain B: P.311 Chain C: P.311 Chain D: P.311 Chain E: P.311 Ligands: CL.12 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
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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