SMTL ID : 8oq7.1

CryoEM structure of human rho1 GABAA receptor in complex with inhibitor TPMPA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x VZA: methyl(1,2,3,6-tetrahydropyridin-4-yl)phosphinic acid(Non-covalent)

VZA.1: 11 residues within 4Å: Chain A: F.159, E.217, S.218, Y.219, Y.262, S.264, T.265, Y.268 Chain B: R.125, M.177, S.189 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.219, A:Y.268 Hydrogen bonds: A:Y.219, A:S.264, A:T.265, B:R.125, B:S.189, B:S.189 VZA.14: 11 residues within 4Å: Chain B: F.159, E.217, S.218, Y.219, Y.262, S.264, T.265, Y.268 Chain C: R.125, M.177, S.189 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:R.125, C:S.189, C:S.189, B:Y.219, B:S.264, B:T.265 Hydrophobic interactions: B:Y.219, B:Y.268 VZA.26: 12 residues within 4Å: Chain C: F.159, E.217, S.218, Y.219, Y.262, S.264, T.265, Y.268 Chain D: Y.123, R.125, M.177, S.189 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.219, C:Y.268 Hydrogen bonds: C:Y.219, C:S.264, C:T.265, D:R.125, D:S.189, D:S.189 VZA.37: 12 residues within 4Å: Chain D: F.159, E.217, S.218, Y.219, Y.262, S.264, T.265, Y.268 Chain E: Y.123, R.125, M.177, S.189 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:Y.219, D:Y.268 Hydrogen bonds: D:Y.219, D:S.264, D:T.265, E:R.125, E:S.189, E:S.189 VZA.48: 11 residues within 4Å: Chain A: R.125, M.177, S.189 Chain E: F.159, E.217, S.218, Y.219, Y.262, S.264, T.265, Y.268 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:Y.219, E:Y.268 Hydrogen bonds: E:Y.219, E:S.264, E:T.265, A:R.125, A:S.189, A:S.189

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

NAG.2: 1 residues within 4Å: Chain A: N.140 No protein-ligand interaction detected (PLIP) 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: 1 residues within 4Å: Chain B: N.140 No protein-ligand interaction detected (PLIP) 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.27: 1 residues within 4Å: Chain C: N.140 No protein-ligand interaction detected (PLIP) NAG.28: 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: 1 residues within 4Å: Chain D: N.140 No protein-ligand interaction detected (PLIP) 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: 1 residues within 4Å: Chain E: N.140 No protein-ligand interaction detected (PLIP) 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)(Non-functional Binders)

HEX.4: 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.5: 2 residues within 4Å: Chain A: L.357, E.361 No protein-ligand interaction detected (PLIP) HEX.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.17: 1 residues within 4Å: Chain B: Y.458 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.458, B:Y.458 HEX.18: 2 residues within 4Å: Chain B: L.357, E.361 No protein-ligand interaction detected (PLIP) HEX.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.29: 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.30: 2 residues within 4Å: Chain C: L.357, E.361 No protein-ligand interaction detected (PLIP) HEX.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.40: 1 residues within 4Å: Chain D: Y.458 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.458, D:Y.458 HEX.41: 2 residues within 4Å: Chain D: L.357, E.361 No protein-ligand interaction detected (PLIP) HEX.42: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.51: 1 residues within 4Å: Chain E: Y.458 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.458, E:Y.458 HEX.52: 2 residues within 4Å: Chain E: L.357, E.361 No protein-ligand interaction detected (PLIP) HEX.53: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

OCT.7: 2 residues within 4Å: Chain A: N.471, L.472 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.472 OCT.20: 2 residues within 4Å: Chain B: N.471, L.472 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.472 OCT.32: 2 residues within 4Å: Chain C: N.471, L.472 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.472 OCT.43: 2 residues within 4Å: Chain D: N.471, L.472 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.472 OCT.54: 2 residues within 4Å: Chain E: N.471, L.472 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.472

10 x D12: DODECANE(Non-covalent)

D12.8: 1 residues within 4Å: Chain A: W.475 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: 1 residues within 4Å: Chain B: W.475 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: 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.290, B:I.341, B:W.349, B:V.353 D12.33: 1 residues within 4Å: Chain C: W.475 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.475, C:W.475, C:W.475 D12.35: 4 residues within 4Å: Chain C: I.341, W.349, V.353 Chain D: F.290 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.341, C:W.349, C:V.353, D:F.290 D12.44: 1 residues within 4Å: Chain D: W.475 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: 3 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:I.341, D:W.349, D:V.353, E:F.290 D12.55: 1 residues within 4Å: Chain E: W.475 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: 1 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:F.290, E:I.341, E:W.349, E:V.353

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 D10.25: 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 D10.34: 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: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.301, D:W.304, D:W.304, C:Y.367 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 E, 1 interactions with chain D Hydrophobic interactions: E:W.304, D:Y.367 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: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 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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