SMTL ID : 5obh.1

Crystal structure of glycine binding protein in complex with bicuculline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-pentamer

Ligands

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.1: 2 residues within 4Å: Chain B: N.87, N.91 No protein-ligand interaction detected (PLIP)

5 x J94: (5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-6-ium(Non-covalent)

J94.2: 9 residues within 4Å: Chain A: E.162, W.164, Y.205, T.208, Y.212 Chain B: F.53, Y.72, R.74, S.135 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.205, A:T.208, B:Y.72 Hydrogen bonds: A:Y.212 Salt bridges: A:E.162 pi-Stacking: A:Y.212 pi-Cation interactions: A:W.164 J94.4: 13 residues within 4Å: Chain B: E.162, W.164, V.165, S.167, Y.205, E.210, Y.212 Chain C: Y.72, R.74, R.96, V.125, M.133, S.135 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:R.96 Water bridges: C:Y.72 pi-Cation interactions: C:R.96, B:W.164, B:Y.212 Hydrophobic interactions: B:W.164, B:Y.205, B:Y.212 Salt bridges: B:E.162 pi-Stacking: B:Y.205 J94.6: 8 residues within 4Å: Chain C: E.162, W.164, Y.205, Y.212 Chain D: F.53, Y.72, R.74, S.135 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.164, C:Y.205, D:Y.72 Salt bridges: C:E.162 pi-Stacking: C:Y.212 pi-Cation interactions: C:W.164 J94.8: 12 residues within 4Å: Chain D: E.162, W.164, V.165, S.167, E.210, Y.212 Chain E: Y.72, R.74, R.96, V.125, M.133, S.135 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:Y.72, D:Y.212 Hydrogen bonds: E:R.96 Salt bridges: D:E.162 pi-Cation interactions: D:W.164, D:Y.212 J94.11: 13 residues within 4Å: Chain A: Y.72, R.74, R.96, V.125, M.133, S.135 Chain E: E.162, W.164, V.165, S.167, Y.205, E.210, Y.212 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain E Hydrogen bonds: A:R.74, A:R.96, E:Y.205 Hydrophobic interactions: E:W.164, E:Y.205, E:Y.212 Salt bridges: E:E.162 pi-Cation interactions: E:W.164, E:Y.212

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

CL.3: 3 residues within 4Å: Chain A: Y.37, I.102, W.103 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: Y.37, I.102, W.103 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain C: Y.37, I.102, W.103 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: Y.37, I.102, W.103 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain E: Y.37, I.102, W.103 Ligand excluded by PLIP

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

NAG.9: 2 residues within 4Å: Chain D: G.90, N.91 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.91 Water bridges: D:N.87 NAG.12: 1 residues within 4Å: Chain E: N.91 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, M.J. et al., A Structural Rationale for N-Methylbicuculline Acting as a Promiscuous Competitive Antagonist of Inhibitory Pentameric Ligand-Gated Ion Channels. Chembiochem (2020)

Release Date

2018-08-01

Peptides

Soluble acetylcholine receptor: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Soluble acetylcholine receptor

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