SMTL ID : 4cof.1

Crystal structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3 homopentamer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.97 Å

Oligo State

homo-pentamer

Ligands

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)(Post Translational Modification)

NAG-NAG-BMA.1: 7 residues within 4Å: Chain A: N.152, E.193, R.195, V.197, R.199, S.214, R.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.195, A:R.199 NAG-NAG-BMA.2: 7 residues within 4Å: Chain B: N.152, E.193, R.195, V.197, R.199, S.214, R.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.195, B:R.199 NAG-NAG-BMA.3: 7 residues within 4Å: Chain C: N.152, E.193, R.195, V.197, R.199, S.214, R.216 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.199 NAG-NAG-BMA.4: 7 residues within 4Å: Chain D: N.152, E.193, R.195, V.197, R.199, S.214, R.216 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.195, D:R.199 NAG-NAG-BMA.5: 7 residues within 4Å: Chain E: N.152, E.193, R.195, V.197, R.199, S.214, R.216 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.195, E:R.199

5 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.6: 8 residues within 4Å: Chain A: Y.100, E.158, S.159, Y.160, F.203, Y.208 Chain E: D.46, Y.65 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain A pi-Stacking: E:Y.65 Hydrophobic interactions: A:F.203, A:F.203 Hydrogen bonds: A:Y.100, A:S.159 BEN.10: 8 residues within 4Å: Chain A: D.46, Y.65 Chain B: Y.100, E.158, S.159, Y.160, F.203, Y.208 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.203, B:F.203, B:F.203 Hydrogen bonds: B:Y.100, B:E.158 pi-Stacking: A:Y.65 BEN.13: 7 residues within 4Å: Chain B: Y.65 Chain C: Y.100, E.158, S.159, Y.160, F.203, Y.208 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain C pi-Stacking: B:Y.65 Hydrophobic interactions: C:F.203, C:F.203, C:F.203 Hydrogen bonds: C:Y.100, C:E.158 BEN.16: 8 residues within 4Å: Chain C: D.46, Y.65 Chain D: Y.100, E.158, S.159, Y.160, F.203, Y.208 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.203, D:F.203, D:F.203 Hydrogen bonds: D:Y.100, D:E.158 pi-Stacking: C:Y.65 BEN.19: 9 residues within 4Å: Chain D: D.46, Y.65 Chain E: Y.100, E.158, S.159, Y.160, F.203, T.205, Y.208 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:Y.100, E:S.159 pi-Stacking: E:F.203, D:Y.65

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

NAG.7: 4 residues within 4Å: Chain A: N.11, S.13, F.14, E.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.14, A:E.17 NAG.9: 5 residues within 4Å: Chain A: Y.69, P.81, L.82, N.83, H.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.69, A:Y.69, A:N.83 NAG.12: 4 residues within 4Å: Chain B: P.81, L.82, N.83, H.122 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.82 Hydrogen bonds: B:N.83 NAG.15: 4 residues within 4Å: Chain C: P.81, L.82, N.83, H.122 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.83 NAG.18: 4 residues within 4Å: Chain D: P.81, L.82, N.83, H.122 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.83 NAG.21: 4 residues within 4Å: Chain E: P.81, L.82, N.83, H.122 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.83

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

CL.8: 5 residues within 4Å: Chain A: F.108, H.110, G.111 Chain B: K.106, S.107 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: H.110, G.111 Chain C: D.104, K.106, S.107 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: F.108, H.110, G.111 Chain D: S.107 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain D: H.110, G.111 Chain E: S.107 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: S.107 Chain E: F.108, H.110, G.111 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, P.S. et al., Crystal Structure of a Human Gabaa Receptor. Nature (2014)

Release Date

2014-06-04

Peptides

GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA-3: 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 BETA-3