SMTL ID : 5osc.1

GLIC-GABAAR alpha1 chimera crystallized in complex with pregnenolone sulfate at pH 4.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-pentamer

Ligands

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: R.76, I.130, E.180 Chain E: I.24, F.41, R.104 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:I.24, E:F.41, A:I.130 Salt bridges: E:R.104, A:R.76 ACT.5: 6 residues within 4Å: Chain A: I.24, F.41, R.104 Chain B: R.76, I.130, E.180 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.130, A:I.24, A:F.41 Salt bridges: B:R.76, A:R.104 ACT.6: 6 residues within 4Å: Chain B: I.72, P.73, E.74, I.75, R.84, Y.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.75 Salt bridges: B:R.84 ACT.11: 6 residues within 4Å: Chain B: I.24, F.41, R.104 Chain C: R.76, I.130, E.180 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.130, B:I.24, B:F.41 Salt bridges: C:R.76, B:R.104 ACT.14: 6 residues within 4Å: Chain C: F.41, R.104 Chain D: R.76, I.130, L.175, E.180 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.41, D:I.130, D:L.175 Salt bridges: C:R.104, D:R.76 ACT.15: 6 residues within 4Å: Chain D: I.72, P.73, E.74, I.75, R.84, Y.101 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.75 Salt bridges: D:R.84 ACT.19: 6 residues within 4Å: Chain D: I.24, F.41, R.104 Chain E: R.76, I.130, E.180 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:I.24, D:F.41, E:I.130 Salt bridges: D:R.104, E:R.76 ACT.20: 4 residues within 4Å: Chain E: I.72, P.73, I.75, R.84 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.75 Salt bridges: E:R.84

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

CL.2: 2 residues within 4Å: Chain A: F.77, R.84 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: F.77, A.83, R.84 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: F.77, A.83, R.84 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain D: F.77, R.84 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain E: F.77, A.83, R.84 Ligand excluded by PLIP

5 x A8W: Pregnenolone sulfate(Non-covalent)

A8W.3: 8 residues within 4Å: Chain A: R.287, I.291, L.294, S.295, A.298, F.299, L.302 Ligands: Y01.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.294, A:A.298, A:F.299 Salt bridges: A:R.287 A8W.8: 8 residues within 4Å: Chain B: R.287, I.291, L.294, S.295, A.298, F.299, L.302 Ligands: Y01.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.298, B:F.299 Salt bridges: B:R.287 A8W.13: 9 residues within 4Å: Chain C: A.265, F.266, S.269, I.291, L.294, S.295, A.298, F.299, L.302 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.266, C:A.298, C:F.299, C:F.299, C:F.299 Hydrogen bonds: C:S.269 A8W.17: 9 residues within 4Å: Chain D: F.266, S.269, R.287, I.291, L.294, S.295, A.298, F.299, L.302 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.298, D:F.299 Hydrogen bonds: D:R.287 A8W.22: 8 residues within 4Å: Chain E: S.269, R.287, I.291, L.294, S.295, A.298, F.299, L.302 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:A.298, E:F.299 Salt bridges: E:R.287

5 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 11 residues within 4Å: Chain A: S.240, D.257, I.260, A.261, Y.264, A.265, F.268, I.272 Chain E: L.202, M.206 Ligands: A8W.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.261, A:Y.264, A:Y.264, A:F.268, A:I.272 Y01.9: 12 residues within 4Å: Chain A: L.202, M.206 Chain B: S.240, D.257, I.260, A.261, Y.264, A.265, F.268, S.269, I.272 Ligands: A8W.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.261, B:Y.264, B:F.268 Hydrogen bonds: B:S.240 Y01.10: 8 residues within 4Å: Chain B: L.202, M.206 Chain C: S.240, I.260, A.261, Y.264, A.265, F.268 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.261, C:A.265, C:F.268 Hydrogen bonds: C:S.240 Y01.18: 10 residues within 4Å: Chain C: L.202, M.206 Chain D: S.240, D.257, I.260, A.261, Y.264, A.265, F.268, I.272 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.261, D:Y.264, D:F.268, C:L.202 Y01.23: 11 residues within 4Å: Chain D: L.202, M.206, I.209 Chain E: S.240, D.257, I.260, A.261, Y.264, A.265, F.268, I.272 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:L.202, E:Y.264, E:Y.264, E:A.265, E:F.268 Hydrogen bonds: E:S.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laverty, D. et al., Crystal structures of a GABAA-receptor chimera reveal new endogenous neurosteroid-binding sites. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-10-11

Peptides

Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-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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Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1

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