SMTL ID : 5afl.1

alpha7-AChBP in complex with lobeline and fragment 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-pentamer

Ligands

1 x NAG- NAG- BMA- BMA: beta-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-BMA.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 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.109, S.110, S.111, H.113 No protein-ligand interaction detected (PLIP) 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: 4 residues within 4Å: Chain E: N.109, S.110, S.111, H.113 No protein-ligand interaction detected (PLIP)

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

L0B.6: 12 residues within 4Å: Chain A: Y.92, S.145, W.146, Y.185, C.187, C.188, Y.192 Chain B: L.37, W.54, Q.56, Q.115, L.117 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.37, B:W.54, B:L.117, A:Y.92, A:W.146, A:W.146, A:W.146, A:Y.192 pi-Stacking: B:W.54, B:W.54 L0B.11: 11 residues within 4Å: Chain B: Y.92, S.145, W.146, C.187, C.188, Y.192 Chain C: L.37, W.54, Q.56, Q.115, L.117 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.37, C:W.54, C:Q.115, C:L.117, B:Y.92, B:W.146, B:Y.192, B:Y.192 pi-Stacking: C:W.54, C:W.54, B:W.146 L0B.12: 11 residues within 4Å: Chain C: Y.92, S.145, W.146, Y.185, C.187, Y.192 Chain D: L.37, W.54, Q.56, Q.115, L.117 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.37, D:W.54, D:L.117, C:Y.92, C:Y.92, C:W.146, C:W.146, C:Y.192 pi-Stacking: D:W.54, D:W.54 L0B.13: 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 E, 4 interactions with chain D Hydrophobic interactions: E:L.37, E:L.117, D:Y.92, D:W.146, D:W.146, D:Y.192 pi-Stacking: E:W.54, E:W.54 L0B.15: 11 residues within 4Å: Chain A: L.37, W.54, Q.115, L.117 Chain E: Y.92, S.145, W.146, Y.185, C.187, C.188, Y.192 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:L.37, A:L.117, E:Y.92, E:W.146, E:Y.192, 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: D.43, N.46, V.48, I.95, R.123 Chain B: M.40, R.121 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.43, A:N.46, A:R.123, B:R.121, B:R.121 Water bridges: A:I.95, B:R.121 GOL.8: 7 residues within 4Å: Chain A: P.17, D.18, I.81, S.82, L.84, W.85, V.86 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.82, A:V.86, A:V.86 Water bridges: A:D.18 GOL.10: 7 residues within 4Å: Chain B: P.17, D.18, I.81, S.82, L.84, W.85, V.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.82, B:V.86, B:V.86 GOL.14: 6 residues within 4Å: Chain D: P.17, I.81, S.82, L.84, W.85, V.86 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.82, D:V.86, D:V.86 GOL.16: 6 residues within 4Å: Chain E: P.17, I.81, S.82, L.84, W.85, V.86 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.82, E:V.86

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.9: 8 residues within 4Å: Chain B: Y.8, L.11, V.12, Y.15, L.64, V.79, S.83, L.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.8, B:S.83

1 x FHV: N-(3-METHYLPHENYL)PYRROLIDINE-1-CARBOXAMIDE(Non-covalent)

FHV.17: 12 residues within 4Å: Chain D: D.18, V.19 Chain E: Q.4, Y.8, L.11, V.12, Y.15, L.64, V.77, S.78, V.79, S.83 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:Q.4, E:Y.8, E:Y.15, E:Y.15, E:L.64, E:V.77, E:V.77, E:V.79, D:D.18, D:V.19

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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