SMTL ID : 8oq6.1

CryoEM structure of human rho1 GABAA receptor apo state

Coordinates

PDB Format

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.22: 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.23: 2 residues within 4Å: Chain C: N.234, H.254 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.255 NAG.31: 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.32: 2 residues within 4Å: Chain D: N.234, H.254 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.255 NAG.40: 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.41: 2 residues within 4Å: Chain E: N.234, H.254 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.255

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

OCT.3: 2 residues within 4Å: Chain A: S.479 Ligands: D10.5 No protein-ligand interaction detected (PLIP) OCT.8: 2 residues within 4Å: Chain A: L.472, W.475 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.472, A:W.475 OCT.15: 2 residues within 4Å: Chain B: S.479 Ligands: D10.17 No protein-ligand interaction detected (PLIP) OCT.20: 2 residues within 4Å: Chain B: L.472, W.475 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.472, B:W.475 OCT.24: 2 residues within 4Å: Chain C: S.479 Ligands: D10.26 No protein-ligand interaction detected (PLIP) OCT.29: 2 residues within 4Å: Chain C: L.472, W.475 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.472, C:W.475 OCT.33: 2 residues within 4Å: Chain D: S.479 Ligands: D10.35 No protein-ligand interaction detected (PLIP) OCT.38: 2 residues within 4Å: Chain D: L.472, W.475 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.472, D:W.475 OCT.42: 2 residues within 4Å: Chain E: S.479 Ligands: D10.44 No protein-ligand interaction detected (PLIP) OCT.47: 2 residues within 4Å: Chain E: L.472, W.475 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.472, E:W.475

15 x D10: DECANE(Non-covalent)

D10.4: 3 residues within 4Å: Chain A: W.304, I.461, P.464 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.304, A:I.461, A:I.461, A:P.464 D10.5: 6 residues within 4Å: Chain A: F.282, T.293, Y.347 Chain E: I.341 Ligands: OCT.3, 7P9.45 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:F.282, E:I.341 D10.9: 3 residues within 4Å: Chain A: W.304 Chain E: A.364, Y.367 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:A.364, E:Y.367, A:W.304 D10.12: 3 residues within 4Å: Chain A: A.364, Y.367 Chain B: W.304 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.304, A:A.364, A:Y.367 D10.16: 3 residues within 4Å: Chain B: W.304, I.461, P.464 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.304, B:I.461, B:I.461, B:P.464 D10.17: 6 residues within 4Å: Chain A: I.341 Chain B: F.282, T.293, Y.347 Ligands: 7P9.6, OCT.15 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.341, B:F.282 D10.21: 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 D10.25: 3 residues within 4Å: Chain C: W.304, I.461, P.464 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.304, C:I.461, C:I.461, C:P.464 D10.26: 5 residues within 4Å: Chain C: F.282, T.293, Y.347 Ligands: 7P9.18, OCT.24 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.282 D10.30: 5 residues within 4Å: Chain C: A.364, Y.367 Chain D: M.297, W.300, W.304 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.300, D:W.304, C:A.364, C:Y.367 D10.34: 3 residues within 4Å: Chain D: W.304, I.461, P.464 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.304, D:I.461, D:I.461, D:P.464 D10.35: 6 residues within 4Å: Chain C: I.341 Chain D: F.282, T.293, Y.347 Ligands: 7P9.27, OCT.33 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.341, D:F.282 D10.39: 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 D10.43: 3 residues within 4Å: Chain E: W.304, I.461, P.464 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:W.304, E:I.461, E:I.461, E:P.464 D10.44: 6 residues within 4Å: Chain D: I.341 Chain E: F.282, T.293, Y.347 Ligands: 7P9.36, OCT.42 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:I.341, E:F.282

10 x 7P9: [(2R)-2-heptanoyloxy-3-phosphonooxy-propyl] nonanoate(Non-covalent)

7P9.6: 7 residues within 4Å: Chain A: I.341, I.346, W.349, F.470, I.473 Chain B: L.286 Ligands: D10.17 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.286, A:I.346, A:W.349, A:F.470, A:I.473 Hydrogen bonds: A:I.341 7P9.7: 5 residues within 4Å: Chain A: A.364, L.368, I.455, Y.458, I.462 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.364, A:Y.458, A:I.462 7P9.18: 7 residues within 4Å: Chain B: I.341, I.346, W.349, F.470, I.473 Chain C: L.286 Ligands: D10.26 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.346, B:W.349, B:F.470, B:I.473, C:L.286 Hydrogen bonds: B:I.341 7P9.19: 5 residues within 4Å: Chain B: A.364, L.368, I.455, Y.458, I.462 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.364, B:Y.458, B:I.462 7P9.27: 7 residues within 4Å: Chain C: I.341, I.346, W.349, F.470, I.473 Chain D: L.286 Ligands: D10.35 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.346, C:W.349, C:F.470, C:I.473, D:L.286 Hydrogen bonds: C:I.341 7P9.28: 5 residues within 4Å: Chain C: A.364, L.368, I.455, Y.458, I.462 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.364, C:Y.458, C:I.462 7P9.36: 7 residues within 4Å: Chain D: I.341, I.346, W.349, F.470, I.473 Chain E: L.286 Ligands: D10.44 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:I.346, D:W.349, D:F.470, D:I.473, E:L.286 Hydrogen bonds: D:I.341 7P9.37: 5 residues within 4Å: Chain D: A.364, L.368, I.455, Y.458, I.462 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.364, D:Y.458, D:I.462 7P9.45: 7 residues within 4Å: Chain A: L.286 Chain E: I.341, I.346, W.349, F.470, I.473 Ligands: D10.5 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:I.346, E:W.349, E:F.470, E:I.473, A:L.286 Hydrogen bonds: E:I.341 7P9.46: 5 residues within 4Å: Chain E: A.364, L.368, I.455, Y.458, I.462 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:A.364, E:Y.458, E:I.462

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

CL.10: 1 residues within 4Å: Chain C: P.311 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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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