SMTL ID : 5j5i.2 (1 other biounit)

X-Ray Crystal Structure of Acetylcholine Binding Protein (AChBP) in Complex with 4-(2-amino-6-{bis[(pyridin-2-yl)methyl]amino}pyrimidin-4-yl)phenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-pentamer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.74, S.76, H.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.76 NAG.7: 3 residues within 4Å: Chain B: N.74, S.76, H.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.76 NAG.10: 3 residues within 4Å: Chain C: N.74, S.76, H.77 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.76 Water bridges: C:N.74 NAG.14: 2 residues within 4Å: Chain D: N.74, S.76 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.76 NAG.19: 3 residues within 4Å: Chain E: N.74, S.76, H.77 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.74, E:S.76, E:H.77

5 x 6GM: 4-(2-amino-6-{bis[(pyridin-2-yl)methyl]amino}pyrimidin-4-yl)phenol(Non-covalent)

6GM.2: 13 residues within 4Å: Chain A: W.151, T.152, Y.193, C.195, C.196, Y.200 Chain B: Q.63, T.64, T.65, R.112, L.120, M.122, Y.172 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Q.63, B:R.112, B:M.122, A:T.152, A:Y.193, A:Y.200, A:Y.200 Hydrogen bonds: B:T.64, B:Y.172, B:Y.172 pi-Stacking: A:W.151 6GM.3: 14 residues within 4Å: Chain A: Q.63, T.64, T.65, R.112, L.120, M.122, Y.172 Chain E: Y.97, W.151, T.152, Y.193, C.195, C.196, Y.200 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:Q.63, A:Q.63, A:R.112, A:M.122, E:Y.97, E:T.152, E:Y.193, E:Y.200 Hydrogen bonds: A:T.64, A:Y.172, A:Y.172 pi-Stacking: E:W.151, E:Y.200 6GM.8: 14 residues within 4Å: Chain B: Y.97, W.151, T.152, Y.193, C.195, C.196, Y.200 Chain C: Q.63, T.64, T.65, R.112, L.120, M.122, Y.172 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:Q.63, C:T.65, C:R.112, C:L.120, C:M.122, B:T.152, B:Y.193 Hydrogen bonds: C:T.64, C:Y.172, C:Y.172 pi-Stacking: B:W.151, B:Y.200 pi-Cation interactions: B:Y.193 6GM.15: 14 residues within 4Å: Chain C: Y.97, W.151, T.152, Y.193, C.195, C.196, Y.200 Chain D: Q.63, T.64, T.65, R.112, L.120, M.122, Y.172 13 PLIP interactions: 7 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:Q.63, D:R.112, D:L.120, D:M.122, C:Y.97, C:T.152, C:Y.193, C:Y.200 Hydrogen bonds: D:T.64, D:Y.172 Water bridges: D:T.65 pi-Stacking: C:W.151, C:Y.200 6GM.16: 14 residues within 4Å: Chain D: Y.97, W.151, T.152, Y.193, C.195, C.196, Y.200 Chain E: Q.63, T.64, T.65, R.112, L.120, M.122, Y.172 12 PLIP interactions: 7 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:Q.63, E:T.65, E:R.112, E:L.120, E:M.122, D:Y.97, D:T.152, D:Y.193 Hydrogen bonds: E:T.64, E:Y.172 pi-Stacking: D:W.151, D:Y.200

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

PO4.4: 7 residues within 4Å: Chain A: D.25, V.26, I.27, H.153 Chain B: R.11, V.82, S.83 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.25, A:D.25, A:I.27, B:S.83 Salt bridges: A:H.153, B:R.11 PO4.5: 7 residues within 4Å: Chain A: R.11, V.82, S.83 Chain E: D.25, V.26, I.27, H.153 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:D.25, E:I.27, A:S.83 Salt bridges: E:H.153, A:R.11 PO4.6: 3 residues within 4Å: Chain A: D.1, D.4, H.77 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.77 PO4.9: 4 residues within 4Å: Chain B: D.1, K.3, D.4, H.77 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.1 Salt bridges: B:K.3, B:H.77 PO4.11: 7 residues within 4Å: Chain C: D.25, V.26, I.27, H.153 Chain D: R.11, V.82, S.83 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.83, C:D.25, C:I.27 Salt bridges: D:R.11, C:H.153 PO4.12: 7 residues within 4Å: Chain B: D.25, V.26, I.27, H.153 Chain C: R.11, V.82, S.83 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.25, B:D.25, B:I.27, C:S.83 Salt bridges: B:H.153, C:R.11 PO4.13: 4 residues within 4Å: Chain C: D.1, K.3, D.4, H.77 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.3, C:H.77 PO4.17: 6 residues within 4Å: Chain C: C.195 Chain D: K.42, Q.63, T.164, E.165, D.168 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.63, D:T.164, D:T.164, D:E.165 Salt bridges: D:K.42 PO4.18: 4 residues within 4Å: Chain D: D.1, K.3, D.4, H.77 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.4 Salt bridges: D:H.77 PO4.20: 7 residues within 4Å: Chain D: D.25, V.26, I.27, H.153 Chain E: R.11, V.82, S.83 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:I.27, E:S.83 Water bridges: D:W.90, D:H.153 Salt bridges: D:H.153, E:R.11 PO4.21: 3 residues within 4Å: Chain E: D.1, D.4, H.77 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:K.3, E:H.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaczanowska, K. et al., Substituted 2-Aminopyrimidines Selective for alpha 7-Nicotinic Acetylcholine Receptor Activation and Association with Acetylcholine Binding Proteins. J. Am. Chem. Soc. (2017)

Release Date

2017-03-08

Peptides

Acetylcholine-binding protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

Acetylcholine-binding protein

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