SMTL ID : 9g7b.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

ABU.1: 9 residues within 4Å: Chain A: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain C: Y.123, R.125, S.189 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.189, C:S.189, A:S.218 Salt bridges: C:R.125 ABU.16: 9 residues within 4Å: Chain A: Y.123, R.125, S.189 Chain B: E.217, S.218, Y.219, Y.262, T.265, Y.268 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.218, A:S.189, A:S.189 Salt bridges: A:R.125 ABU.24: 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: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.189, D:S.189, C:S.218 Salt bridges: D:R.125 ABU.35: 9 residues within 4Å: Chain D: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain E: Y.123, R.125, S.189 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:S.218, E:S.189, E:S.189 Salt bridges: E:R.125 ABU.48: 9 residues within 4Å: Chain B: Y.123, R.125, S.189 Chain E: E.217, S.218, Y.219, Y.262, T.265, Y.268 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:S.189, B:S.189, E:S.218 Salt bridges: B:R.125

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

NAG.2: 1 residues within 4Å: Chain A: N.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.140 NAG.3: 1 residues within 4Å: Chain A: N.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.234 NAG.17: 1 residues within 4Å: Chain B: N.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.140 NAG.18: 1 residues within 4Å: Chain B: N.234 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.234 NAG.25: 1 residues within 4Å: Chain C: N.140 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.140 NAG.26: 1 residues within 4Å: Chain C: N.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.234 NAG.36: 1 residues within 4Å: Chain D: N.140 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.140 NAG.37: 1 residues within 4Å: Chain D: N.234 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.234 NAG.49: 1 residues within 4Å: Chain E: N.140 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.140 NAG.50: 1 residues within 4Å: Chain E: N.234 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.234

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

OCT.4: 4 residues within 4Å: Chain A: W.304 Chain B: A.364, Y.367 Ligands: HEX.23 Ligand excluded by PLIP OCT.7: 2 residues within 4Å: Chain A: S.459, F.463 Ligand excluded by PLIP OCT.10: 2 residues within 4Å: Chain A: W.349 Chain C: L.286 Ligand excluded by PLIP OCT.11: 3 residues within 4Å: Chain A: F.470, I.473, I.477 Ligand excluded by PLIP OCT.14: 2 residues within 4Å: Chain A: L.286 Chain B: W.349 Ligand excluded by PLIP OCT.15: 3 residues within 4Å: Chain B: F.470, I.473, I.477 Ligand excluded by PLIP OCT.19: 4 residues within 4Å: Chain B: W.304 Chain E: A.364, Y.367 Ligands: HEX.56 Ligand excluded by PLIP OCT.22: 2 residues within 4Å: Chain B: S.459, F.463 Ligand excluded by PLIP OCT.27: 3 residues within 4Å: Chain A: Y.367 Chain C: W.304 Ligands: HEX.8 Ligand excluded by PLIP OCT.30: 2 residues within 4Å: Chain C: S.459, F.463 Ligand excluded by PLIP OCT.33: 2 residues within 4Å: Chain C: W.349 Chain D: L.286 Ligand excluded by PLIP OCT.34: 3 residues within 4Å: Chain C: F.470, I.473, I.477 Ligand excluded by PLIP OCT.38: 3 residues within 4Å: Chain C: Y.367 Chain D: W.304 Ligands: HEX.31 Ligand excluded by PLIP OCT.41: 2 residues within 4Å: Chain D: S.459, F.463 Ligand excluded by PLIP OCT.43: 2 residues within 4Å: Chain D: W.349 Chain E: L.286 Ligand excluded by PLIP OCT.44: 3 residues within 4Å: Chain D: F.470, I.473, I.477 Ligand excluded by PLIP OCT.46: 2 residues within 4Å: Chain B: L.286 Chain E: W.349 Ligand excluded by PLIP OCT.47: 3 residues within 4Å: Chain E: F.470, I.473, I.477 Ligand excluded by PLIP OCT.52: 3 residues within 4Å: Chain D: Y.367 Chain E: W.304 Ligands: HEX.42 Ligand excluded by PLIP OCT.55: 2 residues within 4Å: Chain E: S.459, F.463 Ligand excluded by PLIP

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

HEX.5: 2 residues within 4Å: Chain A: W.475, S.479 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.475 HEX.6: 2 residues within 4Å: Chain A: W.304, R.460 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.304 HEX.8: 1 residues within 4Å: Ligands: OCT.27 No protein-ligand interaction detected (PLIP) HEX.20: 2 residues within 4Å: Chain B: W.475, S.479 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.475 HEX.21: 2 residues within 4Å: Chain B: W.304, R.460 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.304 HEX.23: 1 residues within 4Å: Ligands: OCT.4 No protein-ligand interaction detected (PLIP) HEX.28: 2 residues within 4Å: Chain C: W.475, S.479 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.475 HEX.29: 2 residues within 4Å: Chain C: W.304, R.460 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.304 HEX.31: 1 residues within 4Å: Ligands: OCT.38 No protein-ligand interaction detected (PLIP) HEX.39: 2 residues within 4Å: Chain D: W.475, S.479 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.475 HEX.40: 2 residues within 4Å: Chain D: W.304, R.460 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.304 HEX.42: 1 residues within 4Å: Ligands: OCT.52 No protein-ligand interaction detected (PLIP) HEX.53: 2 residues within 4Å: Chain E: W.475, S.479 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.475 HEX.54: 2 residues within 4Å: Chain E: W.304, R.460 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.304 HEX.56: 1 residues within 4Å: Ligands: OCT.19 No protein-ligand interaction detected (PLIP)

5 x 01: 1-[(~{Z})-2-chloranyl-2-(2,4-dichlorophenyl)ethenyl]-1,2,4-triazole

01.9: 12 residues within 4Å: Chain A: I.328, T.329, N.332, W.349, F.352 Chain C: L.286, Q.287, F.290, P.291, G.330, V.331, S.334 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.328 pi-Stacking: A:F.352 Halogen bonds: A:N.332 Hydrogen bonds: C:Q.287, C:Q.287 01.13: 12 residues within 4Å: Chain A: L.286, Q.287, F.290, P.291, G.330, V.331, S.334 Chain B: I.328, T.329, N.332, W.349, F.352 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.328, B:I.328 pi-Stacking: B:F.352 Halogen bonds: B:N.332 Hydrogen bonds: A:Q.287, A:Q.287 01.32: 12 residues within 4Å: Chain C: I.328, T.329, N.332, W.349, F.352 Chain D: L.286, Q.287, F.290, P.291, G.330, V.331, S.334 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Q.287, D:Q.287 Hydrophobic interactions: C:I.328, C:I.328 pi-Stacking: C:F.352 Halogen bonds: C:N.332 01.45: 12 residues within 4Å: Chain B: L.286, Q.287, F.290, P.291, G.330, V.331, S.334 Chain E: I.328, T.329, N.332, W.349, F.352 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:I.328, E:I.328 pi-Stacking: E:F.352 Halogen bonds: E:N.332 Hydrogen bonds: B:Q.287, B:Q.287 01.51: 12 residues within 4Å: Chain D: I.328, T.329, N.332, W.349, F.352 Chain E: L.286, Q.287, F.290, P.291, G.330, V.331, S.334 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:I.328 pi-Stacking: D:F.352 Halogen bonds: D:N.332 Hydrogen bonds: E:Q.287, E:Q.287

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

CL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, C. et al., CryoEM structure of human rho1 GABAA receptor in complex 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
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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