SMTL ID : 4il4.1

The pentameric ligand-gated ion channel GLIC in complex with Se-DDM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-pentamer

Ligands

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

ACT.1: 5 residues within 4Å: Chain A: R.77, I.131, E.181 Chain E: F.42, R.105 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:F.42 Salt bridges: E:R.105, A:R.77 Hydrogen bonds: A:E.181 ACT.7: 5 residues within 4Å: Chain A: I.73, P.74, I.76, R.85, Y.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.76, A:I.76 Salt bridges: A:R.85 ACT.9: 5 residues within 4Å: Chain A: F.42, R.105 Chain B: R.77, I.131, E.181 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.131, A:F.42 Hydrogen bonds: B:E.181 Salt bridges: B:R.77, A:R.105 ACT.12: 7 residues within 4Å: Chain B: I.73, P.74, E.75, I.76, R.85, Y.102, E.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.76, B:I.76 Salt bridges: B:R.85 ACT.14: 5 residues within 4Å: Chain B: F.42, R.105 Chain C: R.77, I.131, E.181 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.131, B:F.42 Salt bridges: C:R.77, B:R.105 ACT.17: 7 residues within 4Å: Chain C: L.45, I.73, P.74, E.75, I.76, R.85, Y.102 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.76 Salt bridges: C:R.85 ACT.19: 6 residues within 4Å: Chain C: I.25, F.42, R.105 Chain D: R.77, I.131, E.181 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.25, C:F.42 Salt bridges: C:R.105, D:R.77 ACT.22: 7 residues within 4Å: Chain D: L.45, 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.25: 5 residues within 4Å: Chain D: F.42, R.105 Chain E: R.77, I.131, E.181 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.42, E:I.131 Salt bridges: D:R.105, E:R.77 Hydrogen bonds: E:E.181 ACT.28: 7 residues within 4Å: Chain E: I.73, P.74, E.75, I.76, R.85, Y.102, E.104 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:I.76, E:I.76 Salt bridges: E:R.85

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

CL.2: 3 residues within 4Å: Chain A: F.78, A.84, R.85 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: N.139, R.179, L.180 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: A.175 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: F.78, R.85 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: F.78, A.84, R.85 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain D: R.77, F.78, R.85 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain E: R.77, F.78, 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.6: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.226 NA.11: 5 residues within 4Å: Chain B: V.5, P.68, I.71, W.72, I.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.73 NA.16: 4 residues within 4Å: Chain C: P.68, I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.68, C:I.73 NA.21: 5 residues within 4Å: Chain D: V.5, P.68, I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.71, D:I.73 NA.27: 4 residues within 4Å: Chain E: P.68, I.71, W.72, I.73 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.73

6 x LSM: dodecyl 4-O-alpha-D-glucopyranosyl-1-seleno-beta-D-glucopyranoside(Non-covalent)(Non-functional Binders)

LSM.8: 10 residues within 4Å: Chain A: I.233, A.237, I.240, L.241, T.244, N.245 Chain B: T.244 Chain E: A.237 Ligands: LSM.24, LSM.29 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:I.233, A:A.237, A:L.241, E:A.237 LSM.13: 7 residues within 4Å: Chain A: A.237 Chain B: I.233, A.237, I.240, L.241, T.244 Ligands: LSM.24 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.233, B:A.237, B:I.240, B:I.240, B:L.241 LSM.18: 7 residues within 4Å: Chain B: A.237 Chain C: I.233, I.236, A.237, I.240, T.244 Ligands: LSM.24 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.233, C:I.236, C:I.240, B:A.237 LSM.23: 8 residues within 4Å: Chain C: I.233, A.234, A.237 Chain D: I.233, A.237, I.240, T.244 Ligands: LSM.24 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.233, D:I.240, D:I.240 LSM.24: 5 residues within 4Å: Ligands: LSM.8, LSM.13, LSM.18, LSM.23, LSM.29 No protein-ligand interaction detected (PLIP) LSM.29: 8 residues within 4Å: Chain E: I.233, A.237, I.240, L.241, T.244, N.245 Ligands: LSM.8, LSM.24 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.233, E:A.237, E:I.240, E:L.241

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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