SMTL ID : 4hfi.1

The GLIC pentameric Ligand-Gated Ion Channel at 2.4 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:F.42, A:I.131 Salt bridges: E:R.105, A:R.77 Hydrogen bonds: A:E.181 ACT.10: 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.13: 5 residues within 4Å: Chain A: F.42, R.105 Chain B: R.77, I.131, E.181 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.181 Salt bridges: B:R.77, A:R.105 Hydrophobic interactions: A:F.42 ACT.19: 7 residues within 4Å: Chain B: I.73, P.74, E.75, I.76, R.85, Y.102, E.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.76, B:I.76 Water bridges: B:Y.102 Salt bridges: B:R.85 ACT.21: 6 residues within 4Å: Chain B: I.25, F.42, R.105 Chain C: R.77, I.131, E.181 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.25, B:F.42, C:I.131 Salt bridges: B:R.105, C:R.77 ACT.27: 7 residues within 4Å: Chain C: L.45, 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 Water bridges: C:I.76 Salt bridges: C:R.85 ACT.29: 6 residues within 4Å: Chain C: I.25, F.42, R.105 Chain D: R.77, I.131, E.181 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.25, C:F.42, D:I.131 Salt bridges: C:R.105, D:R.77 ACT.35: 7 residues within 4Å: Chain D: L.45, I.73, P.74, E.75, I.76, R.85, Y.102 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.76 Salt bridges: D:R.85 ACT.37: 5 residues within 4Å: Chain D: F.42, R.105 Chain E: R.77, I.131, E.181 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:F.42 Salt bridges: D:R.105, E:R.77 Hydrogen bonds: E:E.181 ACT.43: 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 Hydrogen bonds: E:I.76, E:I.76 Water bridges: E:Y.102 Salt bridges: E:R.85

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

PLC.2: 11 residues within 4Å: Chain A: R.118, F.121, Y.194, I.198, I.202, L.206, Y.254, I.258, N.307, F.315 Ligands: PLC.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.121, A:I.198, A:I.202, A:L.206, A:Y.254, A:I.258 PLC.3: 6 residues within 4Å: Chain A: F.210, W.217 Chain B: F.267, I.271, V.275, Y.278 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.210, A:W.217, B:F.267, B:I.271, B:Y.278 PLC.4: 1 residues within 4Å: Ligands: PLC.2 No protein-ligand interaction detected (PLIP) PLC.14: 11 residues within 4Å: Chain B: R.118, F.121, Y.194, I.198, I.202, L.206, Y.254, I.258, N.307, F.315 Ligands: PLC.16 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.121, B:F.121, B:I.198, B:I.202, B:L.206, B:Y.254, B:I.258 Water bridges: B:R.118 PLC.15: 6 residues within 4Å: Chain B: F.210, W.217 Chain C: F.267, I.271, V.275, Y.278 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.210, B:W.217, C:F.267, C:I.271, C:V.275, C:Y.278 PLC.16: 1 residues within 4Å: Ligands: PLC.14 No protein-ligand interaction detected (PLIP) PLC.22: 11 residues within 4Å: Chain C: R.118, F.121, Y.194, I.198, I.202, L.206, Y.254, I.258, N.307, F.315 Ligands: PLC.24 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.121, C:F.121, C:I.198, C:I.202, C:L.206, C:Y.254, C:I.258 PLC.23: 6 residues within 4Å: Chain C: F.210, W.217 Chain D: F.267, I.271, V.275, Y.278 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.267, D:I.271, D:Y.278, C:F.210, C:W.217 PLC.24: 1 residues within 4Å: Ligands: PLC.22 No protein-ligand interaction detected (PLIP) PLC.30: 11 residues within 4Å: Chain D: R.118, F.121, Y.194, I.198, I.202, L.206, Y.254, I.258, N.307, F.315 Ligands: PLC.32 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.121, D:F.121, D:I.198, D:I.202, D:L.206, D:Y.254, D:I.258 Hydrogen bonds: D:R.118, D:Y.254 PLC.31: 6 residues within 4Å: Chain D: F.210, W.217 Chain E: F.267, I.271, V.275, Y.278 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:F.267, E:I.271, E:I.271, E:Y.278, D:F.210, D:W.217 PLC.32: 1 residues within 4Å: Ligands: PLC.30 No protein-ligand interaction detected (PLIP) PLC.38: 11 residues within 4Å: Chain E: R.118, F.121, Y.194, I.198, I.202, L.206, Y.254, I.258, N.307, F.315 Ligands: PLC.40 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.121, E:F.121, E:I.198, E:L.206, E:Y.254, E:I.258 PLC.39: 6 residues within 4Å: Chain A: F.267, I.271, V.275, Y.278 Chain E: F.210, W.217 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:F.267, A:I.271, A:Y.278, E:F.210, E:W.217 PLC.40: 1 residues within 4Å: Ligands: PLC.38 No protein-ligand interaction detected (PLIP)

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

CL.5: 2 residues within 4Å: Chain A: F.78, R.85 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: N.139, R.179, L.180 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: A.175 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: R.77, F.78, R.85 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain C: F.78, A.84, R.85 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain D: R.77, F.78, R.85 Ligand excluded by PLIP CL.41: 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.8: 4 residues within 4Å: Chain A: 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.9: 0 residues within 4Å: (No contacts) 8 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 2 interactions with chain D, 1 interactions with chain E Water bridges: A:T.226, A:T.226, A:T.226, B:T.226, B:T.226, D:T.226, D:T.226, E:T.226 NA.18: 5 residues within 4Å: Chain B: V.5, P.68, I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.71, B:I.73 NA.26: 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.34: 4 residues within 4Å: Chain D: V.5, I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.71, D:I.73 NA.42: 4 residues within 4Å: Chain E: P.68, I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.71, E:I.73

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

LMT.11: 4 residues within 4Å: Ligands: LMT.12, LMT.20, LMT.28, LMT.44 No protein-ligand interaction detected (PLIP) LMT.12: 7 residues within 4Å: Chain A: I.233, A.237, I.240 Chain B: T.244 Chain E: A.237 Ligands: LMT.11, LMT.20 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: E:A.237, A:I.233, A:A.237, A:I.240, B:T.244 LMT.20: 7 residues within 4Å: Chain A: A.237 Chain B: I.233, A.237, L.241 Chain C: T.244 Ligands: LMT.11, LMT.12 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:I.233, B:A.237, B:L.241, A:A.237, C:T.244 LMT.28: 8 residues within 4Å: Chain B: A.237 Chain C: I.233, A.237, I.240, L.241 Chain D: T.244 Ligands: LMT.11, LMT.36 6 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: C:I.233, C:I.240, C:I.240, C:L.241, B:A.237, D:T.244 LMT.36: 5 residues within 4Å: Chain C: A.237 Chain D: I.233, A.237, L.241 Ligands: LMT.28 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.233, C:A.237 LMT.44: 6 residues within 4Å: Chain A: T.244 Chain D: A.237 Chain E: I.233, A.237, I.240 Ligands: LMT.11 6 PLIP interactions: 1 interactions with chain A, 4 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: A:T.244, E:I.233, E:A.237, E:I.240, E:I.240, D:A.237

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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