SMTL ID : 5o87.1 (1 other biounit)

Crystal structure of wild type Aplysia californica AChBP in complex with nicotine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-pentamer

Ligands

5 x NCT: (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE(Non-covalent)

NCT.1: 11 residues within 4Å: Chain A: Y.110, W.164, V.165, Y.205, C.207, C.208, Y.212 Chain B: Y.72, V.125, M.133, I.135 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.164, B:Y.72, B:V.125 Hydrogen bonds: A:Y.110 Water bridges: B:I.135 NCT.10: 11 residues within 4Å: Chain B: Y.110, W.164, V.165, Y.205, C.207, C.208, Y.212 Chain C: Y.72, V.125, M.133, I.135 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:W.164, C:Y.72, C:V.125 pi-Cation interactions: B:Y.205 Water bridges: C:I.135 NCT.20: 11 residues within 4Å: Chain C: Y.110, W.164, V.165, Y.205, C.207, C.208, Y.212 Chain D: Y.72, V.125, M.133, I.135 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.72, D:V.125, C:W.164 Water bridges: D:I.135 NCT.29: 11 residues within 4Å: Chain D: Y.110, W.164, V.165, Y.205, C.207, C.208, Y.212 Chain E: Y.72, V.125, M.133, I.135 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:W.164, E:Y.72 Hydrogen bonds: D:Y.110 pi-Cation interactions: D:Y.205 Water bridges: E:I.135 NCT.39: 11 residues within 4Å: Chain A: Y.72, V.125, M.133, I.135 Chain E: Y.110, W.164, V.165, Y.205, C.207, C.208, Y.212 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:Y.72, A:V.125 Water bridges: A:I.135 Hydrogen bonds: E:Y.110 pi-Cation interactions: E:Y.205

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

NAG.2: 2 residues within 4Å: Chain A: G.90, N.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.91 NAG.11: 1 residues within 4Å: Chain B: N.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.91 NAG.21: 1 residues within 4Å: Chain C: N.91 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.91 NAG.30: 2 residues within 4Å: Chain D: G.90, N.91 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.91 NAG.40: 2 residues within 4Å: Chain E: G.90, N.91 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.91

22 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: A.109, Y.110, S.111, S.112 Chain B: Q.55, V.70, L.119, A.137 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: Y.186, S.188 Chain E: C.144, D.145 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: Q.55, S.184, Y.186 Chain E: M.143 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: P.38, W.103, Y.166 Chain B: R.96, I.123 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain B: A.109, Y.110, S.111, S.112, M.143 Chain C: Q.55, V.70, L.119 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: C.144, D.145, C.157 Chain B: Y.186, S.188 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: M.143 Chain B: Q.55, S.184, Y.186 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: P.38, W.103, Y.166 Chain C: I.123 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: D.29, L.30, R.33, M.83, W.84, Y.89 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain C: A.109, Y.110, S.111, S.112, M.143 Chain D: Q.55, V.70, L.119 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: C.144, D.145 Chain C: Y.186, S.188 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: S.111, M.143 Chain C: Q.55, S.184, Y.186 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain C: P.38, W.103, Y.166 Chain D: K.27, R.96, I.123 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain D: A.109, Y.110, S.111, S.112, M.143 Chain E: Q.55, V.70, L.119, A.137 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain C: D.145, C.157 Chain D: Y.186, S.188 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain C: S.111, M.143 Chain D: Q.55, S.184, Y.186 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain D: P.38, W.103, Y.166 Chain E: K.27, I.123 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain D: D.29, L.30, R.33, M.83, W.84, Y.89 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain A: Q.55, V.70, A.137 Chain E: A.109, Y.110, S.111, S.112 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain D: C.144, D.145, C.157 Chain E: Y.186, S.188 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain D: M.143 Chain E: Q.55, S.184, Y.186 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain A: K.27 Chain E: P.38, W.103, Y.166 Ligand excluded by PLIP

10 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain A: S.167, F.169, E.170, E.210 Chain B: D.94, R.96 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.96 Hydrogen bonds: A:S.167, A:E.210, A:E.210 PO4.6: 5 residues within 4Å: Chain A: K.59, D.68, R.114, S.141 Chain E: R.114 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:D.68, A:R.114, A:S.141 Water bridges: A:K.59, A:R.114, A:R.114, E:R.114 Salt bridges: A:K.59, A:R.139, E:R.114 PO4.14: 6 residues within 4Å: Chain B: S.167, F.169, E.170, E.210 Chain C: D.94, R.96 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Salt bridges: C:R.96 Hydrogen bonds: B:S.167, B:E.210, B:E.210, B:E.210 PO4.15: 6 residues within 4Å: Chain A: R.114 Chain B: K.59, D.68, R.114, R.139, S.141 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.68, B:D.68, B:R.114, B:S.141 Salt bridges: B:K.59, B:R.139, A:R.114 Water bridges: A:R.114, A:R.114, A:R.114 PO4.24: 6 residues within 4Å: Chain C: S.167, F.169, E.170, E.210 Chain D: D.94, R.96 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.167, C:E.170, C:E.210 Salt bridges: D:R.96 PO4.25: 5 residues within 4Å: Chain B: R.114 Chain C: K.59, D.68, R.114, S.141 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.68, C:S.141 Water bridges: C:R.114, C:R.114, C:Q.117, B:R.114 Salt bridges: C:K.59, C:R.139, B:R.114 PO4.33: 6 residues within 4Å: Chain D: S.167, F.169, E.170, E.210 Chain E: D.94, R.96 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:S.167, D:E.170, D:E.210 Water bridges: D:E.210, D:E.210, E:D.94, E:R.96 Salt bridges: E:R.96 PO4.34: 5 residues within 4Å: Chain C: R.114 Chain D: K.59, D.68, R.139, S.141 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.141 Salt bridges: D:K.59, D:R.139, C:R.114 Water bridges: C:R.114, C:R.114 PO4.43: 6 residues within 4Å: Chain A: D.94, R.96 Chain E: S.167, F.169, E.170, E.210 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:S.167, E:S.167, E:S.167, E:E.210, A:D.94 Water bridges: A:R.96 Salt bridges: A:R.96 PO4.44: 5 residues within 4Å: Chain D: R.114 Chain E: K.59, D.68, R.114, S.141 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.141, E:S.141, E:S.141 Water bridges: E:R.114, E:R.114, E:R.114 Salt bridges: E:K.59, E:R.139, D:R.114

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

IPA.9: 5 residues within 4Å: Chain A: Q.20, A.21, N.22, L.23 Chain E: D.43 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:D.43, A:N.22 Hydrogen bonds: A:Q.20, A:N.22, A:L.23 IPA.19: 6 residues within 4Å: Chain A: D.43 Chain B: Q.20, A.21, N.22, L.23, I.92 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.22, B:L.23, B:I.92, A:D.43 Hydrogen bonds: B:Q.20, B:Q.20, B:N.22, B:N.22 IPA.28: 5 residues within 4Å: Chain B: D.43 Chain C: Q.20, A.21, N.22, L.23 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:N.22 Hydrogen bonds: C:N.22, C:L.23 Water bridges: C:Q.20 IPA.38: 5 residues within 4Å: Chain C: D.43 Chain D: Q.20, A.21, N.22, L.23 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.22, D:L.23 IPA.47: 6 residues within 4Å: Chain D: D.43 Chain E: Q.20, A.21, N.22, L.23, I.92 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:N.22, E:I.92 Hydrogen bonds: E:Q.20, E:N.22, E:L.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dawson, A. et al., Engineering a surrogate human heteromeric alpha / beta glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein. Iucrj (2019)

Release Date

2018-06-27

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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