SMTL ID : 8oq8.1

CryoEM structure of human rho1 GABAA receptor in complex with pore blocker picrotoxin

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.138, A:N.140 NAG.2: 3 residues within 4Å: Chain A: N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.255 NAG.12: 2 residues within 4Å: Chain B: T.138, N.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.138 NAG.13: 3 residues within 4Å: Chain B: N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.255 NAG.21: 3 residues within 4Å: Chain C: T.138, N.139, N.140 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.138, C:N.140 NAG.22: 3 residues within 4Å: Chain C: N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.255 NAG.30: 2 residues within 4Å: Chain D: T.138, N.140 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.138 NAG.31: 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:T.255 NAG.39: 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.40: 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:T.255

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

HEX.3: 1 residues within 4Å: Chain A: Y.458 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.458, A:Y.458 HEX.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.14: 2 residues within 4Å: Chain B: Y.458, I.462 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.458, B:Y.458, B:I.462 HEX.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.16: 1 residues within 4Å: Chain B: I.477 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.477 HEX.23: 1 residues within 4Å: Chain C: Y.458 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.458, C:Y.458 HEX.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.25: 2 residues within 4Å: Chain C: F.470, I.473 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.470, C:I.473 HEX.32: 2 residues within 4Å: Chain D: Y.458, I.462 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.458, D:Y.458, D:I.462 HEX.33: 1 residues within 4Å: Chain D: L.357 No protein-ligand interaction detected (PLIP) HEX.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.41: 1 residues within 4Å: Chain E: Y.458 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.458 HEX.42: 1 residues within 4Å: Chain E: L.357 No protein-ligand interaction detected (PLIP) HEX.43: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

10 x D12: DODECANE(Non-covalent)(Non-functional Binders)

D12.6: 3 residues within 4Å: Chain A: T.293, W.475, S.479 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.475 D12.8: 2 residues within 4Å: Chain A: V.353 Chain B: F.290 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.353, B:F.290 D12.17: 4 residues within 4Å: Chain B: L.285, Y.289, T.293, W.475 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.285, B:Y.289, B:W.475 D12.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D12.26: 1 residues within 4Å: Chain C: W.475 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.475 D12.28: 1 residues within 4Å: Chain C: W.349 No protein-ligand interaction detected (PLIP) D12.35: 1 residues within 4Å: Chain D: W.475 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.475, D:W.475 D12.37: 2 residues within 4Å: Chain D: I.341, W.349 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.341 D12.44: 2 residues within 4Å: Chain E: T.293, W.475 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.475 D12.46: 2 residues within 4Å: Chain E: I.341, V.353 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.353

10 x D10: DECANE(Non-covalent)

D10.7: 3 residues within 4Å: Chain A: W.304, R.460, I.461 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.304, A:I.461 D10.9: 3 residues within 4Å: Chain A: M.297, W.304 Chain E: Y.367 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.367 D10.11: 2 residues within 4Å: Chain B: V.301, W.304 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.301 D10.18: 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 D10.20: 1 residues within 4Å: Chain C: W.304 No protein-ligand interaction detected (PLIP) D10.27: 2 residues within 4Å: Chain C: W.304, I.461 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.304 D10.29: 4 residues within 4Å: Chain C: Y.367 Chain D: M.297, V.301, W.304 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.301, C:Y.367 D10.36: 2 residues within 4Å: Chain D: W.304, I.461 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.304 D10.38: 1 residues within 4Å: Chain E: W.304 No protein-ligand interaction detected (PLIP) D10.45: 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

1 x RI5: (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione(Non-covalent)

RI5.10: 10 residues within 4Å: Chain A: P.315, T.319 Chain B: P.315, T.319 Chain C: P.315, T.319 Chain D: P.315, T.319 Chain E: P.315, T.319 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 interactions with chain E, 2 interactions with chain B Hydrogen bonds: C:T.319, B:T.319 Hydrophobic interactions: A:P.315, E:P.315, E:T.319, B:T.319

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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