SMTL ID : 6t9r.1 (1 other biounit)

Aplysia californica AChBP in complex with a cytisine derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-pentamer

Ligands

5 x MXQ: (1~{R},9~{S})-5-(3-oxidanylpropyl)-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one(Non-covalent)

MXQ.1: 15 residues within 4Å: Chain A: Y.110, S.163, W.164, V.165, Y.205, C.207, C.208, Y.212 Chain D: Y.72, R.96, A.124, V.125, M.133, F.134, I.135 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:W.164, A:V.165, A:Y.205, A:Y.212, D:Y.72, D:V.125 Hydrogen bonds: A:W.164 Water bridges: D:I.135 MXQ.8: 15 residues within 4Å: Chain B: Y.110, S.163, W.164, V.165, Y.205, C.207, C.208, Y.212 Chain E: Y.72, R.96, A.124, V.125, M.133, F.134, I.135 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:W.164, B:V.165, B:Y.205, B:Y.212, E:Y.72, E:V.125 Hydrogen bonds: B:W.164 Water bridges: B:W.164 MXQ.19: 16 residues within 4Å: Chain A: Y.72, R.96, I.123, A.124, V.125, M.133, F.134, I.135 Chain C: Y.110, S.163, W.164, V.165, Y.205, C.207, C.208, Y.212 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:W.164, C:V.165, C:Y.205, C:Y.212, A:Y.72, A:V.125 Hydrogen bonds: C:W.164 Water bridges: A:R.96, A:I.135 MXQ.30: 15 residues within 4Å: Chain B: Y.72, R.96, A.124, V.125, M.133, F.134, I.135 Chain D: Y.110, S.163, W.164, V.165, Y.205, C.207, C.208, Y.212 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:W.164, D:V.165, D:Y.205, D:Y.205, D:Y.212, B:V.125 Hydrogen bonds: D:W.164 Water bridges: B:R.96, B:I.135 MXQ.38: 15 residues within 4Å: Chain C: Y.72, R.96, A.124, V.125, M.133, F.134, I.135 Chain E: Y.110, S.163, W.164, V.165, Y.205, C.207, C.208, Y.212 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain E Hydrophobic interactions: C:Y.72, C:V.125, E:W.164, E:V.165, E:Y.205, E:Y.205, E:Y.212 Water bridges: C:I.135 Hydrogen bonds: E:W.164

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

NAG.2: 3 residues within 4Å: Chain A: G.90, N.91 Chain C: D.43 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain B: N.22, G.90, N.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.91 NAG.20: 3 residues within 4Å: Chain C: G.90, N.91 Chain E: D.43 No protein-ligand interaction detected (PLIP) NAG.31: 3 residues within 4Å: Chain D: N.22, G.90, N.91 3 PLIP interactions: 3 interactions with chain D Water bridges: D:G.90, D:G.90, D:N.91 NAG.39: 2 residues within 4Å: Chain E: G.90, N.91 No protein-ligand interaction detected (PLIP)

21 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: Q.55, S.184, Y.186, A.187 Chain C: S.111, M.143, K.160 Ligand excluded by PLIP GOL.5: 9 residues within 4Å: Chain A: P.38, G.39, W.103, Y.166 Chain D: K.27, R.96, T.97, S.98, I.123 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain B: K.42, S.167, F.169, E.170, E.210, Y.212 Chain E: D.94, R.96, V.125 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain B: Q.55, S.184, Y.185, Y.186, A.187 Chain D: S.111, M.143 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain B: T.93, D.94, T.127, H.128 Ligands: GOL.16 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: K.27, S.28, F.31, N.32, T.97, D.101 Ligand excluded by PLIP GOL.15: 12 residues within 4Å: Chain B: P.38, G.39, W.103, T.104, D.106, V.165, Y.166 Chain E: K.27, R.96, T.97, S.98, I.123 Ligand excluded by PLIP GOL.16: 9 residues within 4Å: Chain B: D.94, R.96, V.125 Chain D: K.42, S.167, F.169, E.170, E.210 Ligands: GOL.12 Ligand excluded by PLIP GOL.21: 9 residues within 4Å: Chain A: D.94, R.96 Chain C: K.42, S.167, F.169, E.170, C.208, E.210, Y.212 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain C: Q.55, S.184, Y.185, Y.186, A.187 Chain E: S.111, M.143 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain C: T.93, T.127, H.128 Ligand excluded by PLIP GOL.25: 13 residues within 4Å: Chain A: K.27, R.96, T.97, I.123 Chain C: P.38, G.39, P.40, W.103, T.104, P.105, D.106, V.165, Y.166 Ligand excluded by PLIP GOL.28: 10 residues within 4Å: Chain A: K.42, S.167, F.169, E.170, C.208, E.210, Y.212 Chain D: D.94, R.96, V.125 Ligand excluded by PLIP GOL.29: 9 residues within 4Å: Chain B: K.27, R.96, T.97, S.98, I.123 Chain D: P.38, G.39, W.103, Y.166 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain D: D.178, Q.179, T.197, T.199 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain A: S.111, M.143 Chain D: Q.55, S.184, Y.185, Y.186, A.187 Ligand excluded by PLIP GOL.37: 9 residues within 4Å: Chain C: K.27, R.96, T.97, S.98, I.123 Chain E: P.38, G.39, W.103, Y.166 Ligand excluded by PLIP GOL.40: 9 residues within 4Å: Chain C: D.94, R.96, V.125 Chain E: K.42, S.167, F.169, E.170, E.210, Y.212 Ligand excluded by PLIP GOL.41: 8 residues within 4Å: Chain B: S.111, M.143, K.160 Chain E: Q.55, S.184, Y.185, Y.186, A.187 Ligand excluded by PLIP GOL.43: 9 residues within 4Å: Chain E: E.73, Q.75, T.104, P.105, D.106, I.107, F.134, P.136, Q.138 Ligand excluded by PLIP GOL.44: 8 residues within 4Å: Chain E: L.26, D.29, L.30, R.33, M.83, W.84, D.85, Y.89 Ligand excluded by PLIP

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

PO4.4: 6 residues within 4Å: Chain A: K.59, D.68, R.114, R.139, S.141 Chain C: R.114 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:S.141, A:S.141 Water bridges: A:D.68, A:D.68, A:R.114, A:R.139, A:R.139, C:R.114, C:R.114 Salt bridges: A:K.59, A:R.114, A:R.139, C:R.114 PO4.13: 6 residues within 4Å: Chain B: K.59, D.68, R.114, R.139, S.141 Chain D: R.114 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.114, B:S.141, B:S.141 Water bridges: B:R.114, B:R.139, B:R.139 Salt bridges: B:K.59, B:R.139, D:R.114 PO4.24: 6 residues within 4Å: Chain C: K.59, D.68, R.114, R.139, S.141 Chain E: R.114 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:R.114, C:S.141, C:S.141, C:S.141 Water bridges: C:R.139, C:R.139, E:R.114 Salt bridges: C:K.59, C:R.139, E:R.114 PO4.32: 6 residues within 4Å: Chain A: R.114 Chain D: K.59, D.68, R.114, R.139, S.141 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:D.68, D:D.68, D:R.114, D:S.141 Water bridges: D:K.59, D:K.59, D:R.139, D:R.139 Salt bridges: D:K.59, D:R.139 PO4.42: 6 residues within 4Å: Chain B: R.114 Chain E: K.59, D.68, R.114, R.139, S.141 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:S.141 Water bridges: E:D.68, E:D.68, E:R.139, E:R.139, B:R.114 Salt bridges: E:K.59, E:R.139, B:R.114

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

CL.6: 6 residues within 4Å: Chain A: M.36, Y.37, L.79, L.82, I.102, W.103 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain B: M.36, Y.37, L.79, L.82, I.102, W.103 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain C: Y.37, L.79, L.82, I.102, W.103 Ligand excluded by PLIP CL.35: 6 residues within 4Å: Chain D: M.36, Y.37, L.79, L.82, I.102, W.103 Ligand excluded by PLIP CL.45: 6 residues within 4Å: Chain E: M.36, Y.37, L.79, L.82, I.102, W.103 Ligand excluded by PLIP

5 x K: POTASSIUM ION(Non-covalent)

K.7: 5 residues within 4Å: Chain A: A.99, A.100, I.102, W.103, T.104 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.99, A:I.102, H2O.9, H2O.10 K.18: 5 residues within 4Å: Chain B: A.99, A.100, I.102, W.103, T.104 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.99, B:I.102, B:T.104, H2O.21, H2O.22 K.27: 5 residues within 4Å: Chain C: A.99, A.100, I.102, W.103, T.104 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.99, C:I.102, H2O.29, H2O.34 K.36: 5 residues within 4Å: Chain D: A.99, A.100, I.102, W.103, T.104 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.99, D:I.102, D:T.104, H2O.44, H2O.46 K.46: 5 residues within 4Å: Chain E: A.99, A.100, I.102, W.103, T.104 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:A.99, E:I.102, E:T.104, H2O.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davis, S. et al., The thermodynamic profile and molecular interactions of a C(9)-cytisine derivative-binding acetylcholine-binding protein from Aplysia californica. Acta Crystallogr.,Sect.F (2020)

Release Date

2020-02-12

Peptides

Acetylcholine binding protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

E
EEE

Acetylcholine binding protein

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