SMTL ID : 5afk.1

alpha7-AChBP in complex with lobeline and fragment 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-pentamer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: Y.31, N.109, S.110, S.111, H.113 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.31

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain B: N.109, S.110, S.111, H.113 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.113 NAG-NAG.3: 5 residues within 4Å: Chain C: Y.31, N.109, S.110, S.111, H.113 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.31 NAG-NAG.4: 4 residues within 4Å: Chain D: N.109, S.110, S.111, H.113 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain E: Y.31, N.109, S.110, S.111, H.113 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.31

5 x L0B: Alpha-Lobeline(Non-covalent)

L0B.6: 9 residues within 4Å: Chain A: Y.92, S.145, W.146, Y.185, C.187, Y.192 Chain B: W.54, Q.115, L.117 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.117, A:W.146, A:W.146, A:Y.192, A:Y.192 pi-Stacking: B:W.54, B:W.54 L0B.9: 11 residues within 4Å: Chain B: Y.92, S.145, W.146, Y.185, C.187, C.188, Y.192 Chain C: W.54, Q.56, Q.115, L.117 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.92, B:W.146, B:Y.192, B:Y.192, C:W.54, C:L.117 pi-Stacking: B:W.146, C:W.54, C:W.54 L0B.12: 10 residues within 4Å: Chain C: Y.92, W.146, Y.185, C.187, Y.192 Chain D: L.37, W.54, Q.56, Q.115, L.117 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:Y.92, C:Y.92, C:W.146, C:Y.185, C:Y.192, C:Y.192, D:L.37, D:W.54, D:L.117 pi-Stacking: C:W.146, D:W.54, D:W.54 L0B.16: 11 residues within 4Å: Chain D: Y.92, S.145, W.146, Y.185, C.187, Y.192 Chain E: L.37, W.54, Q.56, Q.115, L.117 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:Y.92, D:W.146, D:W.146, D:Y.192, E:L.37, E:L.117 pi-Stacking: E:W.54, E:W.54 L0B.18: 9 residues within 4Å: Chain A: W.54, Q.115, L.117 Chain E: Y.92, S.145, W.146, C.187, C.188, Y.192 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: A:L.117, E:Y.92, E:W.146, E:Y.192 pi-Stacking: A:W.54, A:W.54, E:W.146

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: L.55, L.89, A.91, P.98, I.120, Q.122, F.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.122, A:Q.122 GOL.10: 7 residues within 4Å: Chain B: L.55, M.57, L.89, P.98, I.120, Q.122, F.143 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.122, B:Q.122 GOL.13: 7 residues within 4Å: Chain C: L.55, M.57, L.89, P.98, I.120, Q.122, F.143 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.122, C:Q.122 GOL.14: 8 residues within 4Å: Chain B: N.46 Chain C: Q.38, I.39, Y.165, I.166, S.169, R.170, F.171 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:I.39, C:Y.165, C:S.169, C:R.170, C:F.171, B:N.46 GOL.19: 6 residues within 4Å: Chain E: L.89, A.91, P.98, I.120, Q.122, F.143 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.122, E:Q.122

6 x 5VU: N-(2,4-difluorophenyl)pyrrolidine-1-carboxamide(Non-covalent)(Covalent)

5VU.8: 14 residues within 4Å: Chain A: Q.4, L.7, Y.8, L.11, V.12, Y.15, L.64, V.77, S.78, V.79, S.83 Chain E: D.18, V.19 Ligands: 5VU.20 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:Y.8, A:L.11, A:V.12, A:Y.15, A:Y.15, A:L.64, A:V.77, A:V.79 Water bridges: E:D.18 5VU.11: 13 residues within 4Å: Chain A: D.18, V.19 Chain B: Q.4, L.7, Y.8, L.11, V.12, Y.15, L.64, V.77, S.78, V.79, S.83 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.8, B:V.12, B:Y.15, B:L.64, B:V.77, B:V.79 5VU.15: 13 residues within 4Å: Chain B: D.18, V.19 Chain C: Q.4, L.7, Y.8, L.11, V.12, Y.15, L.64, V.77, S.78, V.79, S.83 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Y.15, C:Y.15, C:L.64, C:V.77, C:V.79, B:V.19 5VU.17: 12 residues within 4Å: Chain C: D.18, V.19 Chain D: Q.4, L.7, Y.8, V.12, Y.15, L.64, V.77, S.78, V.79, S.83 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.12, D:Y.15, D:L.64, D:V.77, D:V.77, D:V.79 Water bridges: D:Y.8 5VU.20: 13 residues within 4Å: Chain A: Q.4, Q.76, V.77, S.78, L.105 Chain E: D.18, V.19, I.20, W.85, V.86, D.88, H.148 Ligands: 5VU.8 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:Q.4, A:V.77, A:V.77, A:L.105, E:W.85 Hydrogen bonds: A:S.78, A:S.78, E:I.20 5VU.21: 12 residues within 4Å: Chain D: D.18, V.19 Chain E: Q.4, L.7, Y.8, L.11, V.12, L.64, V.77, S.78, V.79, S.83 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.11, E:V.12, E:L.64, E:V.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spurny, R. et al., Molecular Blueprint of Allosteric Binding Sites in a Homologue of the Agonist-Binding Domain of the Alpha7 Nicotinic Acetylcholine Receptor. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-05-06

Peptides

ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7

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