SMTL ID : 3c84.1

Crystal structure of a complex of AChBP from aplysia californica and the neonicotinoid thiacloprid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-pentamer

Ligands

4 x TH4: {(2Z)-3-[(6-chloropyridin-3-yl)methyl]-1,3-thiazolidin-2-ylidene}cyanamide(Non-covalent)

TH4.1: 13 residues within 4Å: Chain A: Y.101, W.155, V.156, Y.196, S.197, C.198, C.199, Y.203 Chain E: Y.63, V.116, M.124, F.125, I.126 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Water bridges: E:Y.63, E:I.126 Halogen bonds: E:M.124 Hydrogen bonds: A:S.197, A:C.198 TH4.3: 13 residues within 4Å: Chain A: Y.63, V.116, M.124, F.125, I.126 Chain B: Y.101, W.155, V.156, Y.196, S.197, C.198, Y.203 Ligands: IPA.4 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.197, B:C.198 Water bridges: A:Y.63, A:I.126 Halogen bonds: A:M.124 TH4.6: 13 residues within 4Å: Chain B: Y.63, V.116, M.124, F.125, I.126 Chain C: Y.101, W.155, V.156, Y.196, S.197, C.198, Y.203 Ligands: IPA.8 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:V.116, B:I.126 Water bridges: B:T.44, B:Y.63, B:I.126 Halogen bonds: B:M.124 Hydrogen bonds: C:S.197, C:C.198 TH4.10: 13 residues within 4Å: Chain C: Y.63, V.116, M.124, F.125, I.126 Chain D: Y.101, W.155, V.156, Y.196, S.197, C.198, Y.203 Ligands: IPA.11 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:S.197, D:C.198 Water bridges: C:T.44, C:Y.63, C:I.126 Halogen bonds: C:M.124

7 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.2: 9 residues within 4Å: Chain A: T.99, Y.101, K.151, F.152, G.153, S.154, W.155, Y.196, D.205 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.101, A:K.151, A:W.155, A:D.205 Hydrogen bonds: A:S.154, A:Y.196 IPA.4: 10 residues within 4Å: Chain B: T.99, A.100, Y.101, F.152, G.153, S.154, W.155, Y.196, D.205 Ligands: TH4.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.155, B:D.205 Hydrogen bonds: B:T.99 IPA.7: 4 residues within 4Å: Chain C: R.191, V.193, P.202, I.204 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.193 Hydrogen bonds: C:R.191, C:R.191 IPA.8: 11 residues within 4Å: Chain C: T.99, Y.101, K.151, F.152, G.153, S.154, W.155, Y.196, I.204, D.205 Ligands: TH4.6 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.101, C:W.155 Hydrogen bonds: C:S.154, C:Y.196 IPA.9: 4 residues within 4Å: Chain C: Q.46, S.175, Y.177 Chain D: Y.101 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Q.46, C:Y.177, D:Y.101 IPA.11: 10 residues within 4Å: Chain D: T.99, A.100, Y.101, F.152, G.153, S.154, W.155, Y.196, D.205 Ligands: TH4.10 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.101, D:W.155, D:D.205 Hydrogen bonds: D:Y.196 IPA.12: 6 residues within 4Å: Chain D: V.116, M.124, F.125, I.126 Chain E: W.155, V.156 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:V.156, D:I.126 Hydrogen bonds: D:I.126 Water bridges: D:I.114

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain C: R.191 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain E: L.70, I.93, W.94 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Talley, T.T. et al., Atomic interactions of neonicotinoid agonists with AChBP: molecular recognition of the distinctive electronegative pharmacophore. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-05-20

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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