SMTL ID : 4ila.1

The pentameric ligand-gated ion channel GLIC A237F in complex with Cesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-pentamer

Ligands

10 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: R.81, I.135, E.185 Chain E: F.46, R.109 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:F.46 Salt bridges: E:R.109, A:R.81 Hydrogen bonds: A:E.185, A:E.185 ACT.2: 6 residues within 4Å: Chain A: L.49, I.77, P.78, I.80, R.89, Y.106 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.77 Hydrogen bonds: A:I.80, A:Y.106 Salt bridges: A:R.89 ACT.16: 5 residues within 4Å: Chain A: F.46, R.109 Chain B: R.81, I.135, E.185 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.135, A:F.46 Hydrogen bonds: B:E.185 Salt bridges: B:R.81, A:R.109 ACT.17: 5 residues within 4Å: Chain B: I.77, P.78, I.80, R.89, Y.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.80 Salt bridges: B:R.89 ACT.29: 5 residues within 4Å: Chain B: F.46, R.109 Chain C: R.81, I.135, E.185 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.46, C:I.135 Salt bridges: B:R.109, C:R.81 Hydrogen bonds: C:E.185 ACT.30: 5 residues within 4Å: Chain C: I.77, P.78, I.80, R.89, Y.106 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.77 Hydrogen bonds: C:I.80, C:Y.106 Salt bridges: C:R.89 ACT.43: 6 residues within 4Å: Chain C: I.29, F.46, R.109 Chain D: R.81, I.135, E.185 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Salt bridges: D:R.81, C:R.109 Hydrophobic interactions: C:I.29, C:F.46 ACT.44: 6 residues within 4Å: Chain D: L.49, I.77, P.78, I.80, R.89, Y.106 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.77 Hydrogen bonds: D:I.80 Salt bridges: D:R.89 ACT.57: 5 residues within 4Å: Chain D: F.46, R.109 Chain E: R.81, I.135, E.185 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.46 Salt bridges: D:R.109, E:R.81 Hydrogen bonds: E:E.185, E:E.185 ACT.58: 6 residues within 4Å: Chain E: L.49, I.77, P.78, I.80, R.89, Y.106 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.80 Salt bridges: E:R.89

10 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)(Non-functional Binders)

PLC.3: 9 residues within 4Å: Chain A: R.122, F.125, Y.198, I.202, L.210, Y.258, N.311, F.319 Ligands: PLC.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.125, A:F.125, A:F.125, A:I.202, A:L.210, A:Y.258 Hydrogen bonds: A:R.122 PLC.4: 1 residues within 4Å: Ligands: PLC.3 No protein-ligand interaction detected (PLIP) PLC.18: 9 residues within 4Å: Chain B: R.122, F.125, Y.198, L.207, Y.258, I.262, N.311, F.319 Ligands: PLC.19 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.125, B:F.125, B:F.125, B:L.207, B:I.262 PLC.19: 1 residues within 4Å: Ligands: PLC.18 No protein-ligand interaction detected (PLIP) PLC.31: 10 residues within 4Å: Chain C: R.122, F.125, Y.198, I.202, I.206, L.210, Y.258, N.311, F.319 Ligands: PLC.32 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.125, C:F.125, C:F.125, C:I.202, C:I.206, C:L.210, C:Y.258 Hydrogen bonds: C:R.122 PLC.32: 1 residues within 4Å: Ligands: PLC.31 No protein-ligand interaction detected (PLIP) PLC.45: 7 residues within 4Å: Chain D: R.122, F.125, Y.198, Y.258, N.311, F.319 Ligands: PLC.46 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.125, D:F.125, D:F.125, D:Y.258 Hydrogen bonds: D:R.122 PLC.46: 1 residues within 4Å: Ligands: PLC.45 No protein-ligand interaction detected (PLIP) PLC.59: 10 residues within 4Å: Chain E: R.122, F.125, Y.198, I.202, I.206, L.210, Y.258, N.311, F.319 Ligands: PLC.60 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.125, E:F.125, E:F.125, E:I.202, E:I.206, E:L.210, E:Y.258 Hydrogen bonds: E:R.122 PLC.60: 1 residues within 4Å: Ligands: PLC.59 No protein-ligand interaction detected (PLIP)

10 x UNL: UNKNOWN LIGAND

UNL.5: 3 residues within 4Å: Chain A: F.271 Chain E: F.214 Ligands: UNL.62 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:F.271, E:F.214 UNL.6: 7 residues within 4Å: Chain A: F.214, W.221 Chain B: I.275, T.278, V.279, Y.282 Ligands: UNL.20 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.275, B:T.278, B:V.279, B:Y.282, A:F.214, A:W.221 UNL.20: 4 residues within 4Å: Chain B: F.271, I.275, V.279 Ligands: UNL.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.271, B:I.275, B:V.279 UNL.21: 9 residues within 4Å: Chain B: F.214, W.217, T.218, W.221 Chain C: I.275, T.278, V.279, Y.282 Ligands: UNL.33 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:W.217, B:T.218, B:W.221, B:W.221, B:W.221, C:I.275, C:T.278, C:Y.282 UNL.33: 4 residues within 4Å: Chain C: F.271, I.275, V.279 Ligands: UNL.21 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.271, C:I.275, C:V.279 UNL.34: 6 residues within 4Å: Chain C: F.214, W.221 Chain D: T.278, V.279, Y.282 Ligands: UNL.47 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:W.221, D:T.278, D:Y.282 UNL.47: 4 residues within 4Å: Chain D: F.271, I.275, V.279 Ligands: UNL.34 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.271, D:V.279 UNL.48: 8 residues within 4Å: Chain D: F.214, T.218, W.221 Chain E: I.275, T.278, V.279, Y.282 Ligands: UNL.61 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.214, D:W.221, D:W.221, E:I.275, E:Y.282, E:Y.282 UNL.61: 5 residues within 4Å: Chain D: F.214 Chain E: F.271, I.275, V.279 Ligands: UNL.48 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:I.275, E:I.275, E:V.279, D:F.214 UNL.62: 8 residues within 4Å: Chain A: I.275, T.278, V.279, Y.282 Chain E: W.217, T.218, W.221 Ligands: UNL.5 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:I.275, A:T.278, A:Y.282, A:Y.282, E:W.217, E:W.221

27 x CS: CESIUM ION(Non-functional Binders)(Non-covalent)

CS.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CS.8: 1 residues within 4Å: Chain A: D.182 Ligand excluded by PLIP CS.9: 3 residues within 4Å: Chain A: Y.27, K.155, D.157 Ligand excluded by PLIP CS.10: 2 residues within 4Å: Chain A: A.91, D.92 Ligand excluded by PLIP CS.11: 1 residues within 4Å: Chain A: V.153 Ligand excluded by PLIP CS.12: 3 residues within 4Å: Chain A: V.9, P.72, I.75 Ligand excluded by PLIP CS.13: 2 residues within 4Å: Chain A: A.88, R.89 Ligand excluded by PLIP CS.22: 3 residues within 4Å: Chain B: Y.27, K.155, D.157 Ligand excluded by PLIP CS.23: 2 residues within 4Å: Chain B: L.150, V.153 Ligand excluded by PLIP CS.24: 2 residues within 4Å: Chain B: A.91, D.92 Ligand excluded by PLIP CS.25: 3 residues within 4Å: Chain B: A.88, R.89, D.90 Ligand excluded by PLIP CS.26: 3 residues within 4Å: Chain B: V.9, P.72, I.75 Ligand excluded by PLIP CS.35: 2 residues within 4Å: Chain C: Y.27, K.155 Ligand excluded by PLIP CS.36: 1 residues within 4Å: Chain C: D.149 Ligand excluded by PLIP CS.37: 3 residues within 4Å: Chain C: V.9, P.72, I.75 Ligand excluded by PLIP CS.38: 2 residues within 4Å: Chain C: A.88, R.89 Ligand excluded by PLIP CS.39: 2 residues within 4Å: Chain C: A.91, D.92 Ligand excluded by PLIP CS.49: 1 residues within 4Å: Chain D: D.182 Ligand excluded by PLIP CS.50: 3 residues within 4Å: Chain D: Y.27, K.155, D.157 Ligand excluded by PLIP CS.51: 3 residues within 4Å: Chain D: V.9, P.72, I.75 Ligand excluded by PLIP CS.52: 2 residues within 4Å: Chain D: A.91, D.92 Ligand excluded by PLIP CS.53: 1 residues within 4Å: Chain D: V.153 Ligand excluded by PLIP CS.54: 2 residues within 4Å: Chain D: A.88, R.89 Ligand excluded by PLIP CS.63: 3 residues within 4Å: Chain E: Y.27, K.155, D.157 Ligand excluded by PLIP CS.64: 2 residues within 4Å: Chain E: A.91, D.92 Ligand excluded by PLIP CS.65: 3 residues within 4Å: Chain E: V.9, P.72, I.75 Ligand excluded by PLIP CS.66: 3 residues within 4Å: Chain E: A.88, R.89, D.90 Ligand excluded by PLIP

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 4 residues within 4Å: Chain A: F.82, V.85, A.88, R.89 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: R.81, F.82, R.89 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain C: F.82, A.88, R.89 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain D: R.81, F.82, R.89 Ligand excluded by PLIP CL.67: 4 residues within 4Å: Chain E: F.82, V.85, A.88, R.89 Ligand excluded by PLIP

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

LMT.15: 5 residues within 4Å: Chain A: F.241, I.244 Chain B: T.248 Ligands: LMT.28, LMT.42 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.248, A:F.241, A:I.244 LMT.28: 5 residues within 4Å: Chain B: F.241, L.245 Chain C: T.248 Ligands: LMT.15, LMT.42 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.241, B:L.245, C:T.248 LMT.41: 3 residues within 4Å: Chain C: F.241, I.244 Ligands: LMT.42 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.241, C:I.244, C:I.244 LMT.42: 9 residues within 4Å: Chain A: F.241 Chain B: F.241 Chain C: F.241 Chain D: F.241 Chain E: F.241 Ligands: LMT.15, LMT.28, LMT.41, LMT.68 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:F.241, C:F.241 LMT.56: 4 residues within 4Å: Chain D: F.241, I.244, L.245 Chain E: T.248 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:T.248, D:F.241, D:I.244 LMT.68: 3 residues within 4Å: Chain E: F.241, I.244 Ligands: LMT.42 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.241, E:I.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauguet, L. et al., Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. Embo J. (2013)

Release Date

2013-02-20

Peptides

Proton-gated ion channel: 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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Proton-gated ion channel

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