SMTL ID : 5afn.1

alpha7-AChBP in complex with lobeline and fragment 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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: 5 residues within 4Å: Chain A: Y.31, H.113 Ligands: NAG.1, BMA.3, MAN.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.31 NAG.7: 5 residues within 4Å: Chain B: N.109, S.110, S.111, H.113 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.109 NAG.8: 1 residues within 4Å: Ligands: NAG.7 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 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.109, C:S.111 Water bridges: C:H.113, C:Q.115 NAG.12: 1 residues within 4Å: Ligands: NAG.11 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.113 NAG.15: 5 residues within 4Å: Chain D: N.109, S.110, S.111, H.113 Ligands: NAG.16 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.109, D:S.111, D:S.111 NAG.16: 1 residues within 4Å: Ligands: NAG.15 No protein-ligand interaction detected (PLIP) NAG.20: 5 residues within 4Å: Chain E: N.109, S.110, S.111, H.113 Ligands: NAG.21 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.109, E:S.111 Water bridges: E:S.110 NAG.21: 1 residues within 4Å: Ligands: NAG.20 No protein-ligand interaction detected (PLIP)

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

BMA.3: 2 residues within 4Å: Ligands: NAG.2, MAN.4 No protein-ligand interaction detected (PLIP)

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

MAN.4: 2 residues within 4Å: Ligands: NAG.2, BMA.3 No protein-ligand interaction detected (PLIP)

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

L0B.5: 11 residues within 4Å: Chain A: Y.92, S.145, W.146, Y.185, C.187, Y.192 Chain B: L.37, W.54, Q.56, Q.115, L.117 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.146, A:W.146, A:Y.192, B:L.37, B:W.54, B:L.117 pi-Stacking: B:W.54, B:W.54 L0B.9: 10 residues within 4Å: Chain B: Y.92, S.145, W.146, C.187, C.188, Y.192 Chain C: W.54, Q.56, Q.115, L.117 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:W.146, B:Y.192, B:Y.192, C:L.117 pi-Stacking: B:W.146, C:W.54, C:W.54 L0B.13: 10 residues within 4Å: Chain C: Y.92, S.145, W.146, Y.185, C.187, Y.192 Chain D: W.54, Q.56, Q.115, L.117 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.92, C:Y.92, C:W.146, C:Y.192, C:Y.192, D:L.117 pi-Stacking: D:W.54, D:W.54 L0B.17: 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 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:L.37, E:L.117, D:Y.92, D:W.146, D:W.146, D:Y.192, D:Y.192 pi-Stacking: E:W.54, E:W.54 L0B.22: 12 residues within 4Å: Chain A: L.37, W.54, Q.56, Q.115, L.117 Chain E: Y.92, S.145, W.146, Y.185, C.187, C.188, Y.192 10 PLIP interactions: 5 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:Y.92, E:W.146, E:Y.192, E:Y.192, A:L.37, A:W.54, A:L.117 pi-Stacking: E:W.146, A:W.54, A:W.54

5 x OJD: (4R)-4-(2-phenylethyl)pyrrolidin-2-one(Non-covalent)

OJD.6: 9 residues within 4Å: Chain A: L.55, M.57, V.86, P.87, L.89, A.91, P.98, Y.116, Q.122 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.55, A:A.91, A:P.98, A:P.98, A:Y.116 Hydrogen bonds: A:P.87 OJD.10: 13 residues within 4Å: Chain B: L.55, M.57, V.86, P.87, D.88, L.89, A.90, A.91, P.98, Y.116, I.120, Q.122, F.143 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.55, B:A.91, B:P.98, B:P.98, B:Y.116, B:I.120, B:F.143 Hydrogen bonds: B:P.87, B:L.89 OJD.14: 11 residues within 4Å: Chain C: L.55, M.57, V.86, P.87, L.89, A.91, P.98, Y.116, I.120, Q.122, F.143 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.55, C:A.91, C:P.98, C:P.98, C:Y.116, C:I.120, C:F.143 Hydrogen bonds: C:P.87 OJD.19: 9 residues within 4Å: Chain D: L.55, M.57, V.86, P.87, L.89, A.91, P.98, I.120, Q.122 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:A.91, D:P.98, D:P.98, D:I.120 Hydrogen bonds: D:P.87, D:L.89 OJD.26: 11 residues within 4Å: Chain E: L.55, M.57, V.86, P.87, L.89, A.91, P.98, Y.116, I.120, Q.122, F.143 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.55, E:A.91, E:P.98, E:P.98, E:Y.116, E:I.120, E:F.143 Hydrogen bonds: E:P.87

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 8 residues within 4Å: Chain D: Y.92, N.93, A.94, S.125 Chain E: L.37, Q.38, V.52, I.166 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:Q.38, D:A.94, D:S.125 Water bridges: E:S.119 GOL.23: 5 residues within 4Å: Chain D: N.16, D.18 Chain E: Y.8, V.12 Ligands: GOL.25 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:N.16, E:Y.8 Water bridges: D:D.18 GOL.24: 9 residues within 4Å: Chain A: L.37, Q.38, V.52, I.166 Chain E: Y.92, N.93, A.94, I.95, S.125 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:S.125, E:S.125 Water bridges: A:S.119 GOL.25: 6 residues within 4Å: Chain E: Y.8, L.11, V.12, V.79, S.83 Ligands: GOL.23 1 PLIP interactions: 1 interactions with chain E Water bridges: E:V.12

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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