SMTL ID : 5afm.1

alpha7-AChBP in complex with lobeline and fragment 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-4-1-mer

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.111, A:S.111 NAG.2: 1 residues within 4Å: Ligands: NAG.1 No protein-ligand interaction detected (PLIP) NAG.6: 5 residues within 4Å: Chain B: N.109, S.110, S.111, H.113 Ligands: NAG.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.111, B:S.111 NAG.7: 2 residues within 4Å: Chain B: H.113 Ligands: NAG.6 No protein-ligand interaction detected (PLIP) NAG.10: 6 residues within 4Å: Chain C: N.109, S.110, S.111, H.113, Q.115 Ligands: NAG.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.111, C:S.111, C:Q.115 NAG.11: 2 residues within 4Å: Chain C: H.113 Ligands: NAG.10 No protein-ligand interaction detected (PLIP) NAG.15: 6 residues within 4Å: Chain D: N.109, S.110, S.111, H.113, Q.115 Ligands: NAG.16 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.111, D:S.111, D:Q.115 NAG.16: 1 residues within 4Å: Ligands: NAG.15 No protein-ligand interaction detected (PLIP) NAG.20: 6 residues within 4Å: Chain E: N.109, S.110, S.111, H.113, Q.115 Ligands: NAG.21 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.111, E:S.111, E:Q.115 Water bridges: E:S.110 NAG.21: 2 residues within 4Å: Chain E: H.113 Ligands: NAG.20 No protein-ligand interaction detected (PLIP)

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

L0B.3: 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, S.119 Ligands: GOL.4 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.37, A:Y.92, A:W.146, A:Y.192, A:Y.192 pi-Stacking: B:W.54 L0B.8: 10 residues within 4Å: Chain B: Y.92, W.146, Y.185, C.187, Y.192 Chain C: L.37, 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:W.146, B:Y.192, B:Y.192, C:L.37, C:W.54, C:L.117 pi-Stacking: C:W.54 L0B.12: 10 residues within 4Å: Chain C: Y.92, S.145, W.146, Y.185, C.187, C.188, Y.192 Chain D: W.54, Q.115, L.117 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Y.92, C:Y.92, C:W.146, C:W.146, C:Y.192, C:Y.192, D:W.54, D:L.117 pi-Stacking: C:W.146, D:W.54, D:W.54 L0B.17: 13 residues within 4Å: Chain D: Y.92, S.145, W.146, Y.185, C.187, C.188, Y.192 Chain E: L.37, W.54, Q.115, L.117, S.119 Ligands: GOL.18 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:L.37, E:W.54, E:W.54, E:L.117, D:W.146, D:W.146, D:Y.192 pi-Stacking: E:W.54, D:W.146 L0B.22: 12 residues within 4Å: Chain A: L.37, W.54, Q.56, Q.115, L.117, S.119 Chain E: Y.92, S.145, W.146, Y.185, C.187, Y.192 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: A:L.37, A:W.54, A:L.117, E:Y.92, E:W.146, E:Y.192 pi-Stacking: A:W.54, A:W.54, E:W.146

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: Y.92, N.93, A.94, I.95, S.125 Chain B: Q.38, V.52, I.166 Ligands: L0B.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.94, A:S.125 GOL.13: 9 residues within 4Å: Chain C: Y.92, N.93, A.94, I.95, S.125 Chain D: L.37, Q.38, V.52, I.166 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.38, C:Y.92, C:A.94 Water bridges: D:S.119 GOL.18: 8 residues within 4Å: Chain D: Y.92, N.93, A.94, I.95, S.125 Chain E: Q.38, I.166 Ligands: L0B.17 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:Q.38, D:S.125 GOL.23: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.38

5 x 9Z0: 4,5-dibromo-N-(3-hydroxypropyl)-1H-pyrrole-2-carboxamide(Non-covalent)

9Z0.5: 15 residues within 4Å: Chain A: F.32, F.53, L.55, L.89, A.90, A.91, K.97, P.98, I.120, Q.122, F.143 Chain B: V.100, L.101, T.102, P.103 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.89, A:A.91, A:Q.122, A:Q.122, B:V.100 9Z0.9: 13 residues within 4Å: Chain B: F.32, F.53, L.55, L.89, A.91, P.98, I.120, Q.122, F.143 Chain C: V.100, L.101, T.102, P.103 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:L.89, B:Q.122, B:Q.122, C:V.100 9Z0.14: 12 residues within 4Å: Chain C: F.32, F.53, L.55, L.89, A.90, A.91, P.98, I.120, Q.122, F.143 Chain D: L.101, P.103 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.89, C:A.91, C:Q.122, C:Q.122 9Z0.19: 13 residues within 4Å: Chain D: F.32, F.53, L.55, L.89, A.91, P.98, I.120, Q.122, F.143 Chain E: V.100, L.101, T.102, P.103 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:L.89, D:Q.122, D:Q.122, E:T.102 Water bridges: D:A.91, D:A.91 9Z0.24: 12 residues within 4Å: Chain A: V.100, L.101, T.102 Chain E: F.32, F.53, L.55, L.89, A.91, P.98, I.120, Q.122, F.143 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:L.89, E:Q.122, E:Q.122, A:V.100

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: ACDE
ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

E
E

B
B

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

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

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