SMTL ID : 4bfq.1

Assembly of a triple pi-stack of ligands in the binding site of Aplysia californica acetylcholine binding protein (AChBP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-pentamer

Ligands

14 x 083: 4,6-dimethyl-N'-(3-pyridin-2-ylisoquinolin-1-yl)pyrimidine-2-carboximidamide(Non-covalent)

083.1: 7 residues within 4Å: Chain A: Y.91, Y.186, C.188, C.189, Y.193 Chain B: S.164 Ligands: 083.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.91, A:Y.91, A:Y.186, A:Y.193, A:Y.193 Hydrogen bonds: A:Y.186 pi-Stacking: A:Y.186, A:Y.186 083.2: 8 residues within 4Å: Chain A: Y.91, S.144, W.145, Y.193 Chain B: Y.53, S.164 Ligands: 083.1, 083.3 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.91, A:Y.91, A:W.145, A:W.145 pi-Stacking: A:Y.91 Hydrogen bonds: B:S.165, B:S.165 083.3: 9 residues within 4Å: Chain A: V.146 Chain B: T.34, Y.53, Q.55, V.106, M.114, I.116, D.162 Ligands: 083.2 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.53 Hydrogen bonds: B:T.34, B:Q.55 083.4: 10 residues within 4Å: Chain B: Y.91, S.144, Y.186, C.188, C.189, Y.193 Chain C: Y.53, D.162, S.164 Ligands: 083.5 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:Y.53, B:Y.91, B:Y.91, B:Y.186, B:Y.193 Hydrogen bonds: C:Y.53, C:Y.53 pi-Stacking: B:Y.186, B:Y.186 083.5: 4 residues within 4Å: Chain B: W.145 Chain C: Y.53, Q.55 Ligands: 083.4 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Y.53, B:W.145 083.6: 7 residues within 4Å: Chain C: Y.91, Q.184, Y.186, C.188, Y.193 Chain D: S.164 Ligands: 083.7 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.91, C:Y.91, C:Y.186, C:Y.193 Hydrogen bonds: C:Y.186 pi-Stacking: C:Y.186, C:Y.186 083.7: 9 residues within 4Å: Chain C: Y.91, S.144, W.145, Y.193 Chain D: Y.53, D.162, S.164 Ligands: 083.6, 083.8 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.91, C:Y.91, C:W.145, D:Y.53 pi-Stacking: C:Y.91 083.8: 6 residues within 4Å: Chain C: V.146 Chain D: Q.55, R.77, V.106, M.114 Ligands: 083.7 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.106 083.9: 6 residues within 4Å: Chain D: Y.91, Y.186, C.188, Y.193 Chain E: S.164 Ligands: 083.10 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.91, D:Y.193 Hydrogen bonds: D:Y.186 pi-Stacking: D:Y.186, D:Y.186 083.10: 9 residues within 4Å: Chain D: Y.91, S.144, W.145, Y.193 Chain E: Y.53, D.162, S.164 Ligands: 083.9, 083.11 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.91, D:W.145 pi-Stacking: D:Y.91 083.11: 7 residues within 4Å: Chain D: V.146 Chain E: Q.55, R.77, V.106, M.114, I.116 Ligands: 083.10 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.116 Hydrogen bonds: E:D.162 083.13: 7 residues within 4Å: Chain A: S.164 Chain E: Y.91, Y.186, C.188, C.189, Y.193 Ligands: 083.14 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Y.91, E:Y.193, E:Y.193 Hydrogen bonds: E:Y.186 pi-Stacking: E:Y.186, E:Y.186 083.14: 9 residues within 4Å: Chain A: Y.53, D.162, S.164 Chain E: Y.91, S.144, W.145, Y.193 Ligands: 083.13, 083.15 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:Y.91, E:Y.91, E:W.145, E:W.145, A:Y.53 pi-Stacking: E:Y.91 083.15: 8 residues within 4Å: Chain A: Y.53, Q.55, R.77, V.106, M.114, I.116 Chain E: V.146 Ligands: 083.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:Y.53, A:I.116, E:V.146

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 9 residues within 4Å: Chain D: M.17, Y.18, P.19, W.84, Y.147 Chain E: K.8, R.77, S.79, I.104 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:K.8, E:K.8, E:S.79, D:W.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stornaiuolo, M. et al., Assembly of a Pi-Pi Stack of Ligands in the Binding Site of an Acetylcholine Binding Protein. Nat.Commun. (2013)

Release Date

2013-05-22

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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