SMTL ID : 4zzb.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-pentamer

Ligands

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

LMT.1: 8 residues within 4Å: Chain A: I.233, I.240 Chain B: I.233, I.240 Chain C: I.240 Chain D: I.240 Chain E: I.240 Ligands: XE.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.233

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

CL.2: 4 residues within 4Å: Chain A: F.78, V.81, A.84, R.85 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: F.78, V.81, A.84, R.85 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain C: F.78, V.81, A.84, R.85 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain D: R.77, F.78, A.84, R.85 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain E: F.78, A.84, R.85 Ligand excluded by PLIP

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

NA.3: 4 residues within 4Å: Chain A: V.5, P.68, E.69, I.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.71 NA.12: 3 residues within 4Å: Chain B: V.5, P.68, I.71 No protein-ligand interaction detected (PLIP) NA.20: 2 residues within 4Å: Chain C: P.68, I.71 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.68 NA.27: 3 residues within 4Å: Chain D: V.5, P.68, I.71 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.69 NA.34: 4 residues within 4Å: Chain E: V.5, P.68, E.69, I.71 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.69

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

ACT.4: 6 residues within 4Å: Chain A: L.45, I.73, P.74, I.76, R.85, Y.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.76 Salt bridges: A:R.85 ACT.13: 5 residues within 4Å: Chain B: I.73, P.74, E.75, I.76, R.85 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.73 Hydrogen bonds: B:I.76 Salt bridges: B:R.85 ACT.18: 7 residues within 4Å: Chain C: I.25, F.42, R.105 Chain D: R.77, V.79, I.131, E.181 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.79, D:I.131 Salt bridges: D:R.77, C:R.105 ACT.21: 5 residues within 4Å: Chain C: I.73, P.74, 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.28: 7 residues within 4Å: Chain D: I.73, P.74, E.75, I.76, R.85, Y.102, E.104 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.76 Salt bridges: D:R.85 ACT.35: 6 residues within 4Å: Chain E: P.74, E.75, I.76, R.85, Y.102, E.104 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.76 Salt bridges: E:R.85

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

XE.5: 1 residues within 4Å: Ligands: LMT.1 Ligand excluded by PLIP XE.6: 4 residues within 4Å: Chain A: F.207, I.211 Chain B: L.232, Y.263 Ligand excluded by PLIP XE.7: 4 residues within 4Å: Chain A: L.232, Y.263 Chain E: F.207, I.211 Ligand excluded by PLIP XE.8: 3 residues within 4Å: Chain A: Y.197, T.255, I.259 Ligand excluded by PLIP XE.9: 5 residues within 4Å: Chain A: F.37, L.126, I.128, F.165, L.188 Ligand excluded by PLIP XE.10: 3 residues within 4Å: Chain A: A.298, F.299, V.302 Ligand excluded by PLIP XE.14: 4 residues within 4Å: Chain B: F.207, I.211 Chain C: L.232, Y.263 Ligand excluded by PLIP XE.15: 2 residues within 4Å: Chain B: T.255, I.259 Ligand excluded by PLIP XE.16: 5 residues within 4Å: Chain B: F.37, L.126, I.128, F.165, L.188 Ligand excluded by PLIP XE.17: 2 residues within 4Å: Chain B: A.298, V.302 Ligand excluded by PLIP XE.22: 4 residues within 4Å: Chain C: F.207, I.211 Chain D: L.232, Y.263 Ligand excluded by PLIP XE.23: 2 residues within 4Å: Chain C: T.255, I.259 Ligand excluded by PLIP XE.24: 5 residues within 4Å: Chain C: F.37, L.126, I.128, F.165, L.188 Ligand excluded by PLIP XE.25: 1 residues within 4Å: Chain C: F.299 Ligand excluded by PLIP XE.29: 4 residues within 4Å: Chain D: F.207, I.211 Chain E: L.232, Y.263 Ligand excluded by PLIP XE.30: 3 residues within 4Å: Chain D: Y.197, T.255, I.259 Ligand excluded by PLIP XE.31: 6 residues within 4Å: Chain D: F.37, L.126, I.128, F.165, Y.186, L.188 Ligand excluded by PLIP XE.32: 2 residues within 4Å: Chain D: F.299, V.302 Ligand excluded by PLIP XE.36: 2 residues within 4Å: Chain E: T.255, I.259 Ligand excluded by PLIP XE.37: 5 residues within 4Å: Chain E: F.37, L.126, I.128, F.165, L.188 Ligand excluded by PLIP XE.38: 3 residues within 4Å: Chain E: A.298, F.299, V.302 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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