SMTL ID : 3eam.1

An open-pore structure of a bacterial pentameric ligand-gated ion channel

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-pentamer

Ligands

6 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.1: 13 residues within 4Å: Chain A: K.33, I.233, A.237, I.240, L.241, T.244, N.245 Chain B: K.33, T.244 Chain E: A.237 Ligands: LMT.6, LMT.9, LMT.18 9 PLIP interactions: 6 interactions with chain A, 1 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: A:I.233, A:I.240, A:L.241, E:A.237 Hydrogen bonds: A:T.244, A:T.244, A:N.245, B:K.33 Salt bridges: B:K.33 LMT.6: 9 residues within 4Å: Chain A: A.237 Chain B: A.237, I.240, T.244, N.245 Chain C: K.33, T.244 Ligands: LMT.1, LMT.9 7 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: B:I.240, A:A.237 Hydrogen bonds: B:T.244, B:T.244, B:T.244, C:K.33, C:K.33 LMT.9: 11 residues within 4Å: Chain A: S.230 Chain B: S.230 Chain C: S.230, I.233 Chain D: S.230 Chain E: S.230 Ligands: LMT.1, LMT.6, LMT.11, LMT.17, LMT.18 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:S.230, D:S.230, B:S.230, B:S.230, A:S.230 LMT.11: 9 residues within 4Å: Chain B: A.237 Chain C: A.237, I.240, T.244, N.245 Chain D: K.33, T.244 Ligands: LMT.9, LMT.17 12 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: B:A.237, D:T.244, C:A.237, C:I.240, C:I.240 Hydrogen bonds: D:K.33, C:T.244, C:T.244, C:N.245, C:N.245 Water bridges: D:K.248 Salt bridges: D:K.33 LMT.17: 12 residues within 4Å: Chain C: A.237 Chain D: I.233, A.237, I.240, L.241, T.244, N.245 Chain E: K.33, T.244 Ligands: LMT.9, LMT.11, LMT.18 10 PLIP interactions: 7 interactions with chain D, 2 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: D:I.233, D:A.237, D:I.240, D:I.240, D:L.241, C:A.237 Hydrogen bonds: D:T.244, D:T.244, E:T.244 Salt bridges: E:K.33 LMT.18: 10 residues within 4Å: Chain A: K.33 Chain D: A.237 Chain E: D.31, A.237, I.240, T.244, N.245 Ligands: LMT.1, LMT.9, LMT.17 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:A.237, E:A.237, E:I.240 Hydrogen bonds: E:T.244, E:T.244, E:N.245

15 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.2: 8 residues within 4Å: Chain A: F.121, Y.194, I.198, L.203, Y.254, N.307, F.315 Ligands: PC1.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.121, A:Y.194, A:I.198, A:L.203, A:Y.254 Hydrogen bonds: A:Y.194 PC1.3: 7 residues within 4Å: Chain A: F.265, R.287, I.291, A.294, S.295, F.299 Ligands: PC1.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.265, A:A.294, A:F.299 PC1.4: 10 residues within 4Å: Chain A: I.271, T.274, V.275, Y.278, E.282, Q.284 Chain E: F.210, W.217, R.296 Ligands: PC1.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:I.271, A:T.274, A:V.275, E:W.217 Hydrogen bonds: A:Q.284 PC1.5: 11 residues within 4Å: Chain A: F.210, W.217, R.296, L.304 Chain B: V.275, Y.278, E.282, Q.284, R.287 Ligands: PC1.2, PC1.8 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.275, B:Y.278, A:W.217, A:L.304 Hydrogen bonds: B:Q.284 PC1.7: 8 residues within 4Å: Chain B: R.118, Y.194, I.198, L.203, Y.254, I.258, N.307, F.315 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.198, B:L.203, B:Y.254, B:I.258 Hydrogen bonds: B:R.118, B:Y.194 PC1.8: 8 residues within 4Å: Chain B: F.265, E.272, S.290, I.291, A.294, S.295, F.299 Ligands: PC1.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.265, B:E.272, B:A.294 PC1.10: 11 residues within 4Å: Chain B: F.210, W.217, P.300 Chain C: I.271, V.275, Y.278, L.279, E.282, Q.284, R.287 Ligands: PC1.13 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.271, C:Y.278, B:F.210, B:W.217, B:W.217, B:P.300 Hydrogen bonds: C:R.287 PC1.12: 11 residues within 4Å: Chain C: F.121, S.191, Y.194, I.198, I.202, L.203, L.206, Y.254, I.258, N.307, F.315 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.121, C:F.121, C:Y.194, C:I.198, C:I.202, C:L.203, C:L.206, C:Y.254, C:I.258 Hydrogen bonds: C:Y.194 Salt bridges: C:E.163 PC1.13: 9 residues within 4Å: Chain C: F.265, V.268, R.287, I.291, A.294, S.295, A.298, F.299 Ligands: PC1.10 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.265, C:V.268, C:A.298, C:F.299 Salt bridges: C:R.287 PC1.14: 11 residues within 4Å: Chain C: F.210, W.217, F.303 Chain D: I.271, V.275, Y.278, L.279, E.282, Q.284, R.287 Ligands: PC1.16 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:I.271, D:V.275, D:Y.278, C:F.210, C:W.217, C:W.217, C:W.217, C:F.303 PC1.15: 8 residues within 4Å: Chain D: F.121, Y.194, I.198, L.203, Y.254, I.258, N.307, F.315 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.121, D:F.121, D:F.121, D:I.198, D:L.203, D:Y.254, D:I.258 Hydrogen bonds: D:Y.194 PC1.16: 9 residues within 4Å: Chain D: F.265, V.268, R.287, I.291, A.294, S.295, A.298, F.299 Ligands: PC1.14 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.265, D:V.268, D:A.298 Salt bridges: D:R.287 PC1.19: 11 residues within 4Å: Chain D: F.210, W.217 Chain E: I.271, T.274, V.275, Y.278, L.279, E.282, Q.284, R.287 Ligands: PC1.21 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:T.274, E:V.275, E:Y.278, D:W.217, D:W.217, D:W.217 Hydrogen bonds: E:Q.284 Salt bridges: E:R.287 PC1.20: 8 residues within 4Å: Chain E: R.118, F.121, S.191, Y.194, Y.254, I.258, N.307, F.315 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.121, E:Y.194, E:I.258 Hydrogen bonds: E:R.118 PC1.21: 8 residues within 4Å: Chain E: F.265, R.287, I.291, A.294, A.298, F.299, V.302 Ligands: PC1.19 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.265, E:A.298, E:V.302, E:V.302 Salt bridges: E:R.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bocquet, N. et al., X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation. Nature (2009)

Release Date

2008-11-04

Peptides

Glr4197 protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Glr4197 protein

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