SMTL ID : 9g55.1

CryoEM structure of human rho1 GABAA receptor in complex with neurosteroid THDOC

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: 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.2: 2 residues within 4Å: Chain A: N.234, H.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.255 NAG.13: 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.14: 2 residues within 4Å: Chain B: N.234, H.254 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.255 NAG.24: 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.25: 2 residues within 4Å: Chain C: N.234, H.254 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.255 NAG.35: 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.36: 2 residues within 4Å: Chain D: N.234, H.254 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.255 NAG.46: 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.47: 2 residues within 4Å: Chain E: N.234, H.254 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.255

5 x A8Z: Tetrahydrodeoxycorticosterone(Non-covalent)

A8Z.3: 7 residues within 4Å: Chain A: L.207, L.285, Y.289, T.293, W.475, S.479 Ligands: HEX.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.285, A:W.475, A:W.475, A:W.475 Hydrogen bonds: A:Y.289, A:T.293 A8Z.15: 7 residues within 4Å: Chain B: L.207, L.285, Y.289, T.293, W.475, S.479 Ligands: HEX.20 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.285, B:W.475, B:W.475, B:W.475 Hydrogen bonds: B:Y.289, B:T.293 A8Z.26: 7 residues within 4Å: Chain C: L.207, L.285, Y.289, T.293, W.475, S.479 Ligands: HEX.31 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.285, C:W.475, C:W.475, C:W.475 Hydrogen bonds: C:Y.289, C:T.293 A8Z.37: 7 residues within 4Å: Chain D: L.207, L.285, Y.289, T.293, W.475, S.479 Ligands: HEX.42 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.285, D:W.475, D:W.475, D:W.475 Hydrogen bonds: D:Y.289, D:T.293 A8Z.48: 7 residues within 4Å: Chain E: L.207, L.285, Y.289, T.293, W.475, S.479 Ligands: HEX.53 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:L.285, E:W.475, E:W.475, E:W.475 Hydrogen bonds: E:Y.289, E:T.293

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

HEX.4: 1 residues within 4Å: Chain A: Y.458 Ligand excluded by PLIP HEX.5: 1 residues within 4Å: Chain A: L.357 Ligand excluded by PLIP HEX.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HEX.8: 3 residues within 4Å: Chain A: F.282 Ligands: A8Z.3, OCT.55 Ligand excluded by PLIP HEX.16: 1 residues within 4Å: Chain B: Y.458 Ligand excluded by PLIP HEX.17: 1 residues within 4Å: Chain B: L.357 Ligand excluded by PLIP HEX.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HEX.20: 3 residues within 4Å: Chain B: F.282 Ligands: OCT.10, A8Z.15 Ligand excluded by PLIP HEX.27: 1 residues within 4Å: Chain C: Y.458 Ligand excluded by PLIP HEX.28: 1 residues within 4Å: Chain C: L.357 Ligand excluded by PLIP HEX.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HEX.31: 3 residues within 4Å: Chain C: F.282 Ligands: OCT.22, A8Z.26 Ligand excluded by PLIP HEX.38: 1 residues within 4Å: Chain D: Y.458 Ligand excluded by PLIP HEX.39: 1 residues within 4Å: Chain D: L.357 Ligand excluded by PLIP HEX.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HEX.42: 3 residues within 4Å: Chain D: F.282 Ligands: OCT.33, A8Z.37 Ligand excluded by PLIP HEX.49: 1 residues within 4Å: Chain E: Y.458 Ligand excluded by PLIP HEX.50: 1 residues within 4Å: Chain E: L.357 Ligand excluded by PLIP HEX.51: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HEX.53: 3 residues within 4Å: Chain E: F.282 Ligands: OCT.44, A8Z.48 Ligand excluded by PLIP

5 x D12: DODECANE(Non-covalent)

D12.7: 3 residues within 4Å: Chain A: N.471, L.472, W.475 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.471, A:L.472, A:W.475 D12.19: 3 residues within 4Å: Chain B: N.471, L.472, W.475 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.471, B:L.472, B:W.475 D12.30: 3 residues within 4Å: Chain C: N.471, L.472, W.475 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.471, C:L.472, C:W.475 D12.41: 3 residues within 4Å: Chain D: N.471, L.472, W.475 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:N.471, D:L.472, D:W.475 D12.52: 3 residues within 4Å: Chain E: N.471, L.472, W.475 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:N.471, E:L.472, E:W.475

10 x D10: DECANE(Non-covalent)

D10.9: 2 residues within 4Å: Chain A: W.304, I.461 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.304, A:I.461 D10.11: 1 residues within 4Å: Chain E: Y.367 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.367 D10.12: 1 residues within 4Å: Chain A: Y.367 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.367 D10.21: 2 residues within 4Å: Chain B: W.304, I.461 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.304, B:I.461 D10.23: 1 residues within 4Å: Chain B: Y.367 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.367 D10.32: 2 residues within 4Å: Chain C: W.304, I.461 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.304, C:I.461 D10.34: 3 residues within 4Å: Chain C: Y.367 Chain D: W.300, V.301 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.367, D:W.300, D:V.301 D10.43: 2 residues within 4Å: Chain D: W.304, I.461 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.304, D:I.461 D10.45: 1 residues within 4Å: Chain D: Y.367 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.367 D10.54: 2 residues within 4Å: Chain E: W.304, I.461 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.304, E:I.461

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

OCT.10: 1 residues within 4Å: Ligands: HEX.20 No protein-ligand interaction detected (PLIP) OCT.22: 1 residues within 4Å: Ligands: HEX.31 No protein-ligand interaction detected (PLIP) OCT.33: 2 residues within 4Å: Chain D: L.286 Ligands: HEX.42 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.286 OCT.44: 1 residues within 4Å: Ligands: HEX.53 No protein-ligand interaction detected (PLIP) OCT.55: 1 residues within 4Å: Ligands: HEX.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, C. et al., Cryo-EM structures of Rho1 GABAA receptors with neurosteroid. To Be Published

Release Date

2025-07-30

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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