SMTL ID : 5afj.1

alpha7-AChBP in complex with lobeline and fragment 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-pentamer

Ligands

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.1: 5 residues within 4Å: Chain A: N.109, S.110, S.111, H.113 Ligands: NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.109, A:S.111, A:S.111 NAG.2: 1 residues within 4Å: Ligands: NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.60 NAG.6: 4 residues within 4Å: Chain B: N.109, S.111, H.113 Ligands: NAG.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.109, B:S.111 NAG.7: 1 residues within 4Å: Ligands: NAG.6 No protein-ligand interaction detected (PLIP) NAG.11: 5 residues within 4Å: Chain C: N.109, S.110, S.111, H.113 Ligands: NAG.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.111 Water bridges: C:N.109, C:N.109 NAG.12: 1 residues within 4Å: Ligands: NAG.11 No protein-ligand interaction detected (PLIP) NAG.17: 5 residues within 4Å: Chain D: N.109, S.110, S.111, H.113 Ligands: NAG.18 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.109, D:S.111, D:S.111, D:H.113 NAG.18: 2 residues within 4Å: Ligands: NAG.17, BMA.19 No protein-ligand interaction detected (PLIP) NAG.25: 5 residues within 4Å: Chain E: N.109, S.110, S.111, H.113 Ligands: NAG.26 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.109, E:S.111, E:S.111 NAG.26: 2 residues within 4Å: Chain E: T.60 Ligands: NAG.25 No protein-ligand interaction detected (PLIP)

10 x 42R: (3S)-6-(4-bromophenyl)-3-hydroxy-1,3-dimethyl-2,3-dihydropyridin-4(1H)-one(Non-covalent)

42R.3: 10 residues within 4Å: Chain A: L.7, E.10, L.11, N.14, Y.63, L.64, Q.65, W.66, Y.71, V.77 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.7, A:L.11, A:L.64, A:W.66 Hydrogen bonds: A:Y.71 42R.4: 10 residues within 4Å: Chain A: Y.92, N.93, I.95, S.125, K.142, Y.185 Chain B: L.37, Q.38, I.166 Ligands: L0B.5 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.37, B:I.166, B:I.166 Hydrogen bonds: A:K.142, A:K.142 Water bridges: A:Y.185 42R.8: 8 residues within 4Å: Chain B: L.7, E.10, L.11, L.64, Q.65, W.66, Y.71, V.77 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.7, B:L.11, B:L.64, B:W.66 Hydrogen bonds: B:E.10, B:Y.71 42R.9: 11 residues within 4Å: Chain B: Y.92, N.93, I.95, K.142, Y.185 Chain C: L.37, Q.38, V.52, W.54, I.166 Ligands: L0B.10 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.37, C:W.54, C:I.166, B:N.93 Hydrogen bonds: B:K.142, B:K.142 42R.13: 9 residues within 4Å: Chain C: L.7, E.10, L.11, Y.63, L.64, Q.65, W.66, Y.71, V.77 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.10, C:E.10, C:L.64, C:W.66 42R.14: 10 residues within 4Å: Chain C: Y.92, N.93, I.95, S.125, K.142, R.183 Chain D: L.37, Q.38, I.166 Ligands: L0B.15 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:N.93, D:L.37, D:I.166 Hydrogen bonds: C:K.142, C:K.142 Halogen bonds: D:Q.38 42R.21: 13 residues within 4Å: Chain D: L.7, E.10, L.11, N.14, Y.63, L.64, Q.65, W.66, E.70, Y.71, V.77, V.79, V.108 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.7, D:L.7, D:E.10, D:L.11, D:L.64, D:W.66 42R.22: 10 residues within 4Å: Chain D: Y.92, N.93, I.95, S.125, K.142, R.183, Y.185 Chain E: Q.38, I.166 Ligands: L0B.23 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:N.93, E:I.166 Hydrogen bonds: D:K.142, D:K.142, D:Y.185 42R.27: 11 residues within 4Å: Chain E: L.7, E.10, L.11, N.14, Y.63, L.64, W.66, Y.71, V.77, V.79, V.108 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.7, E:L.7, E:E.10, E:L.11, E:L.64, E:W.66 Hydrogen bonds: E:Y.71 Water bridges: E:Q.65 42R.28: 11 residues within 4Å: Chain A: L.37, V.52, I.166 Chain E: Y.92, N.93, I.95, S.125, K.142, R.183, Y.185 Ligands: L0B.29 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:L.37, A:I.166, E:N.93 Hydrogen bonds: E:K.142, E:K.142, E:R.183, E:Y.185

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

L0B.5: 13 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 Ligands: 42R.4 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.92, A:Y.92, A:W.146, A:Y.192, A:Y.192, B:L.37, B:W.54, B:Q.115, B:L.117 pi-Stacking: A:W.146, B:W.54, B:W.54 L0B.10: 15 residues within 4Å: Chain B: Y.92, S.145, W.146, T.147, Y.185, C.187, C.188, Y.192 Chain C: W.54, L.105, L.107, Q.115, Y.116, L.117 Ligands: 42R.9 15 PLIP interactions: 8 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:W.54, C:W.54, C:W.54, C:L.107, C:Q.115, C:L.117, C:L.117, C:L.117, B:W.146, B:W.146, B:T.147, B:Y.185, B:Y.192, B:Y.192 Water bridges: B:E.186 L0B.15: 12 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 Ligands: 42R.14 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.37, D:W.54, D:L.117, C:W.146, C:W.146, C:Y.192 pi-Stacking: D:W.54, D:W.54 L0B.23: 10 residues within 4Å: Chain D: Y.92, W.146, C.187, C.188, Y.192 Chain E: L.37, W.54, Q.115, L.117 Ligands: 42R.22 12 PLIP interactions: 6 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:L.37, E:W.54, E:W.54, E:L.117, D:Y.92, D:Y.92, D:W.146, D:W.146, D:Y.192, D:Y.192 pi-Stacking: E:W.54, E:W.54 L0B.29: 12 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 Ligands: 42R.28 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:L.37, A:W.54, A:L.117, 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 Water bridges: E:Y.192

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 4 residues within 4Å: Chain C: M.57, L.89, P.98, Y.116 3 PLIP interactions: 3 interactions with chain C Water bridges: C:A.91, C:Q.122, C:Q.122 GOL.24: 7 residues within 4Å: Chain D: L.55, M.57, L.89, P.98, I.120, Q.122, F.143 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.122, D:Q.122 GOL.30: 7 residues within 4Å: Chain E: L.55, L.89, A.91, P.98, I.120, Q.122, F.143 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.122, E:Q.122 Water bridges: E:L.89, E:A.91

1 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.19: 2 residues within 4Å: Ligands: NAG.18, MAN.20 No protein-ligand interaction detected (PLIP)

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.20: 1 residues within 4Å: Ligands: BMA.19 No protein-ligand interaction detected (PLIP)

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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