SMTL ID : 4zzc.1

The GLIC pentameric Ligand-Gated Ion Channel open form complexed to xenon

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-pentamer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: I.25, F.42, R.105 Chain B: R.77, I.131, E.181 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.181 Salt bridges: B:R.77, A:R.105 Hydrophobic interactions: A:I.25, A:F.42 ACT.6: 6 residues within 4Å: Chain A: L.45, I.73, P.74, I.76, R.85, Y.102 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.73 Hydrogen bonds: A:I.76 Salt bridges: A:R.85 ACT.15: 6 residues within 4Å: Chain B: I.25, F.42, R.105 Chain C: R.77, I.131, E.181 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.105, C:R.77 ACT.20: 6 residues within 4Å: Chain B: L.45, I.73, P.74, I.76, R.85, Y.102 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.73 Hydrogen bonds: B:I.76 Salt bridges: B:R.85 ACT.28: 5 residues within 4Å: Chain C: F.42, R.105 Chain D: R.77, I.131, E.181 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.42 Salt bridges: C:R.105, D:R.77 Hydrogen bonds: D:E.181 ACT.34: 6 residues within 4Å: Chain C: I.73, P.74, E.75, I.76, R.85, Y.102 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.76, C:I.76 Salt bridges: C:R.85 ACT.42: 5 residues within 4Å: Chain D: F.42, R.105 Chain E: R.77, I.131, E.181 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:E.181 Salt bridges: E:R.77, D:R.105 ACT.47: 6 residues within 4Å: Chain D: I.73, P.74, E.75, I.76, R.85, Y.102 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.76, D:I.76 Salt bridges: D:R.85 ACT.55: 5 residues within 4Å: Chain A: R.77, I.131, E.181 Chain E: F.42, R.105 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:I.131 Hydrogen bonds: A:E.181 Salt bridges: A:R.77, E:R.105 ACT.60: 7 residues within 4Å: Chain E: I.73, P.74, E.75, I.76, R.85, Y.102, E.104 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.73 Hydrogen bonds: E:I.76, E:I.76 Salt bridges: E:R.85

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

PLC.2: 10 residues within 4Å: Chain A: R.118, F.121, Y.194, I.202, L.206, Y.254, I.258, N.307, F.315 Ligands: PLC.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.121, A:F.121, A:F.121, A:Y.194, A:I.202, A:L.206, A:Y.254, A:I.258 Hydrogen bonds: A:R.118 PLC.3: 1 residues within 4Å: Ligands: PLC.2 No protein-ligand interaction detected (PLIP) PLC.16: 10 residues within 4Å: Chain B: R.118, F.121, Y.194, I.202, L.206, Y.254, I.258, N.307, F.315 Ligands: PLC.17 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.121, B:F.121, B:F.121, B:Y.194, B:I.202, B:L.206, B:Y.254, B:I.258 PLC.17: 1 residues within 4Å: Ligands: PLC.16 No protein-ligand interaction detected (PLIP) PLC.29: 10 residues within 4Å: Chain C: R.118, F.121, Y.194, I.202, L.206, Y.254, I.258, N.307, F.315 Ligands: PLC.30 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.121, C:F.121, C:F.121, C:I.202, C:L.206, C:Y.254, C:I.258 Hydrogen bonds: C:R.118 PLC.30: 1 residues within 4Å: Ligands: PLC.29 No protein-ligand interaction detected (PLIP) PLC.43: 9 residues within 4Å: Chain D: R.118, F.121, Y.194, L.206, Y.254, I.258, N.307, F.315 Ligands: PLC.44 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.121, D:F.121, D:F.121, D:Y.194, D:L.206, D:Y.254, D:I.258 Hydrogen bonds: D:R.118 PLC.44: 1 residues within 4Å: Ligands: PLC.43 No protein-ligand interaction detected (PLIP) PLC.56: 10 residues within 4Å: Chain E: R.118, F.121, Y.194, I.202, L.206, Y.254, I.258, N.307, F.315 Ligands: PLC.57 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.121, E:F.121, E:F.121, E:I.202, E:L.206, E:Y.254, E:I.258 Hydrogen bonds: E:R.118 PLC.57: 1 residues within 4Å: Ligands: PLC.56 No protein-ligand interaction detected (PLIP)

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

CL.4: 4 residues within 4Å: Chain A: R.77, F.78, V.81, R.85 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: R.77, F.78, V.81, R.85 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain C: F.78, V.81, R.85 Ligand excluded by PLIP CL.45: 4 residues within 4Å: Chain D: R.77, F.78, V.81, R.85 Ligand excluded by PLIP CL.58: 4 residues within 4Å: Chain E: R.77, F.78, V.81, R.85 Ligand excluded by PLIP

6 x NA: SODIUM ION(Non-functional Binders)

NA.5: 5 residues within 4Å: Chain A: V.5, P.68, I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.68, A:I.73 NA.19: 4 residues within 4Å: Chain B: P.68, I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.68, B:I.73 NA.32: 4 residues within 4Å: Chain C: V.5, P.68, E.69, I.71 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.68 NA.33: 1 residues within 4Å: Chain C: T.226 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.226, C:T.226 NA.46: 4 residues within 4Å: Chain D: V.5, P.68, I.71, I.73 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.73 NA.59: 3 residues within 4Å: Chain E: P.68, E.69, I.71 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.71

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

LMT.7: 5 residues within 4Å: Ligands: LMT.8, LMT.21, LMT.35, LMT.48, LMT.61 No protein-ligand interaction detected (PLIP) LMT.8: 5 residues within 4Å: Chain A: A.237, I.240 Chain E: A.237 Ligands: LMT.7, LMT.21 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:A.237, A:I.240, A:I.240, E:A.237 LMT.21: 6 residues within 4Å: Chain A: A.237 Chain B: A.237, I.240, L.241 Ligands: LMT.7, LMT.8 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.237, B:A.237, B:I.240, B:I.240, B:L.241 LMT.35: 5 residues within 4Å: Chain B: A.237 Chain C: A.237, I.240 Ligands: LMT.7, LMT.48 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:A.237, C:A.237, C:I.240, C:I.240 LMT.48: 7 residues within 4Å: Chain C: A.237 Chain D: A.237, I.240, L.241, T.244 Ligands: LMT.7, LMT.35 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.237, D:I.240, C:A.237 LMT.61: 5 residues within 4Å: Chain D: A.237 Chain E: I.233, A.237, I.240 Ligands: LMT.7 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:I.233, E:A.237, E:I.240, D:A.237

30 x XE: XENON(Non-covalent)(Non-functional Binders)

XE.9: 4 residues within 4Å: Chain A: V.229, L.232, I.233 Chain E: T.231 Ligand excluded by PLIP XE.10: 4 residues within 4Å: Chain A: P.120, Y.197, I.201, T.255 Ligand excluded by PLIP XE.11: 4 residues within 4Å: Chain A: I.202, Y.254, T.255, I.258 Ligand excluded by PLIP XE.12: 2 residues within 4Å: Chain A: V.270, V.273 Ligand excluded by PLIP XE.13: 4 residues within 4Å: Chain A: F.37, I.128, F.165, L.188 Ligand excluded by PLIP XE.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP XE.22: 3 residues within 4Å: Chain B: V.229, L.232, I.233 Ligand excluded by PLIP XE.23: 4 residues within 4Å: Chain B: P.120, Y.197, I.201, T.255 Ligand excluded by PLIP XE.24: 4 residues within 4Å: Chain B: I.202, Y.254, T.255, I.258 Ligand excluded by PLIP XE.25: 2 residues within 4Å: Chain B: V.270, V.273 Ligand excluded by PLIP XE.26: 5 residues within 4Å: Chain B: F.37, I.128, F.165, Y.186, L.188 Ligand excluded by PLIP XE.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP XE.36: 4 residues within 4Å: Chain B: T.231 Chain C: V.229, L.232, I.233 Ligand excluded by PLIP XE.37: 3 residues within 4Å: Chain C: Y.197, I.201, T.255 Ligand excluded by PLIP XE.38: 4 residues within 4Å: Chain C: I.202, Y.254, T.255, I.258 Ligand excluded by PLIP XE.39: 2 residues within 4Å: Chain C: V.270, V.273 Ligand excluded by PLIP XE.40: 4 residues within 4Å: Chain C: F.37, I.128, F.165, L.188 Ligand excluded by PLIP XE.41: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP XE.49: 3 residues within 4Å: Chain C: T.231 Chain D: L.232, I.233 Ligand excluded by PLIP XE.50: 4 residues within 4Å: Chain D: P.120, Y.197, I.201, T.255 Ligand excluded by PLIP XE.51: 4 residues within 4Å: Chain D: I.202, Y.254, T.255, I.258 Ligand excluded by PLIP XE.52: 1 residues within 4Å: Chain D: V.270 Ligand excluded by PLIP XE.53: 4 residues within 4Å: Chain D: F.37, I.128, F.165, L.188 Ligand excluded by PLIP XE.54: 1 residues within 4Å: Chain D: V.302 Ligand excluded by PLIP XE.62: 3 residues within 4Å: Chain E: V.229, L.232, I.233 Ligand excluded by PLIP XE.63: 4 residues within 4Å: Chain E: P.120, Y.197, I.201, T.255 Ligand excluded by PLIP XE.64: 5 residues within 4Å: Chain E: F.121, I.202, Y.254, T.255, I.258 Ligand excluded by PLIP XE.65: 2 residues within 4Å: Chain E: V.270, V.273 Ligand excluded by PLIP XE.66: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP XE.67: 5 residues within 4Å: Chain E: L.126, I.128, F.165, Y.186, L.188 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauguet, L. et al., Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel. Plos One (2016)

Release Date

2016-03-02

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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