SMTL ID : 5osa.1

GLIC-GABAAR alpha1 chimera crystallized at pH4.6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 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 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:I.24, E:F.41 Salt bridges: E:R.104, A:R.76 ACT.2: 4 residues within 4Å: Chain A: I.72, P.73, I.75, R.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.75 Salt bridges: A:R.84 ACT.8: 6 residues within 4Å: Chain A: I.24, F.41, R.104 Chain B: R.76, I.130, E.180 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.24, A:F.41 Salt bridges: A:R.104, B:R.76 ACT.13: 6 residues within 4Å: Chain B: I.24, F.41, R.104 Chain C: R.76, I.130, E.180 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.24, B:F.41, C:I.130 Salt bridges: B:R.104, C:R.76 ACT.14: 4 residues within 4Å: Chain C: I.72, P.73, I.75, R.84 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.75 Salt bridges: C:R.84 ACT.18: 5 residues within 4Å: Chain C: F.41, R.104 Chain D: R.76, I.130, E.180 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.130, C:F.41 Salt bridges: D:R.76, C:R.104 ACT.19: 5 residues within 4Å: Chain D: I.72, P.73, 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.24: 6 residues within 4Å: Chain D: I.24, F.41, R.104 Chain E: R.76, I.130, E.180 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:I.24, D:F.41 Salt bridges: D:R.104, E:R.76

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

CL.3: 3 residues within 4Å: Chain A: F.77, A.83, R.84 Ligand excluded by PLIP CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: F.77, A.83, R.84 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: F.77, A.83, R.84 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain D: F.77, A.83, R.84 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain E: F.77, A.83, R.84 Ligand excluded by PLIP

8 x D12: DODECANE(Non-covalent)

D12.6: 8 residues within 4Å: Chain A: A.265, F.266, S.269, I.291, L.294, S.295, A.298, F.299 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.294 D12.10: 8 residues within 4Å: Chain B: Y.193, I.205, I.209, F.303, G.304, N.307, W.311, L.315 No protein-ligand interaction detected (PLIP) D12.11: 8 residues within 4Å: Chain B: V.262, A.265, F.266, S.269, L.294, S.295, A.298, F.299 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.265, B:F.266 D12.16: 8 residues within 4Å: Chain C: A.265, F.266, S.269, I.291, L.294, S.295, A.298, F.299 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.265 D12.21: 8 residues within 4Å: Chain D: A.265, F.266, S.269, I.291, L.294, S.295, A.298, F.299 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.266, D:I.291 D12.22: 9 residues within 4Å: Chain D: Y.193, V.197, I.205, I.209, F.303, G.304, N.307, W.311, L.315 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:N.307, D:W.311, D:L.315 D12.26: 8 residues within 4Å: Chain E: V.262, A.265, F.266, S.269, L.294, S.295, A.298, F.299 No protein-ligand interaction detected (PLIP) D12.27: 8 residues within 4Å: Chain E: Y.193, V.197, I.205, F.303, G.304, N.307, W.311, L.315 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:Y.193, E:F.303, E:W.311, E:W.311, E:L.315

5 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 11 residues within 4Å: Chain A: S.240, D.257, I.260, A.261, Y.264, A.265, F.268, I.272 Chain E: I.198, L.202, M.206 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:A.261, A:A.265, A:F.268, A:F.268, E:L.202 Hydrogen bonds: A:S.240, A:D.257 Y01.12: 12 residues within 4Å: Chain A: I.198, L.202, M.206, I.209 Chain B: S.240, D.257, I.260, A.261, Y.264, A.265, F.268, I.272 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.261, B:A.265, B:F.268, B:F.268 Hydrogen bonds: B:S.240, B:D.257 Y01.17: 10 residues within 4Å: Chain B: L.202, M.206 Chain C: S.240, D.257, I.260, A.261, Y.264, A.265, F.268, I.272 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.261, C:Y.264, C:A.265, C:F.268, B:L.202 Hydrogen bonds: C:S.240, C:D.257 Y01.23: 12 residues within 4Å: Chain C: I.198, L.202, M.206 Chain D: S.240, D.257, I.260, A.261, Y.264, A.265, F.268, S.269, I.272 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.202, D:A.261, D:A.265, D:F.268, D:F.268 Hydrogen bonds: D:S.240, D:D.257 Y01.28: 12 residues within 4Å: Chain D: I.198, L.202, M.206 Chain E: S.240, D.257, I.260, A.261, Y.264, A.265, F.268, S.269, I.272 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:I.260, E:Y.264, E:A.265, E:F.268, D:L.202 Hydrogen bonds: E:S.240, E:D.257

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-1,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-1,Gamma-aminobutyric acid receptor subunit alpha-1

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