SMTL ID : 4il9.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.83 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: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:E.185, A:E.185 Salt bridges: A:R.81, E:R.109 Hydrophobic interactions: E:F.46 ACT.2: 7 residues within 4Å: Chain A: L.49, I.77, P.78, E.79, I.80, R.89, Y.106 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.77 Hydrogen bonds: A:I.80 Salt bridges: A:R.89 ACT.13: 5 residues within 4Å: Chain A: F.46, R.109 Chain B: R.81, I.135, E.185 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.46, B:I.135 Salt bridges: A:R.109, B:R.81 Hydrogen bonds: B:E.185 ACT.14: 6 residues within 4Å: Chain B: L.49, I.77, P.78, I.80, R.89, Y.106 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.77 Hydrogen bonds: B:I.80 Salt bridges: B:R.89 ACT.23: 5 residues within 4Å: Chain B: F.46, R.109 Chain C: R.81, I.135, E.185 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.135, B:F.46 Hydrogen bonds: C:E.185 Salt bridges: C:R.81, B:R.109 ACT.24: 6 residues within 4Å: Chain C: I.77, P.78, E.79, I.80, R.89, Y.106 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.77 Hydrogen bonds: C:I.80 Salt bridges: C:R.89 ACT.34: 6 residues within 4Å: Chain C: I.29, F.46, R.109 Chain D: R.81, I.135, E.185 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.29, C:F.46 Salt bridges: C:R.109, D:R.81 ACT.35: 5 residues within 4Å: Chain D: I.77, P.78, I.80, R.89, Y.106 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.80 Salt bridges: D:R.89 ACT.45: 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.46: 8 residues within 4Å: Chain E: L.49, I.77, P.78, E.79, I.80, R.89, Y.106, E.108 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:I.77 Hydrogen bonds: E:I.80 Salt bridges: E:R.89

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

PLC.3: 11 residues within 4Å: Chain A: R.122, F.125, Y.198, I.202, I.206, L.207, Y.258, I.262, N.311, F.319 Ligands: PLC.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.125, A:F.125, A:I.206, A:L.207, A:Y.258, A:I.262 Hydrogen bonds: A:R.122 PLC.4: 1 residues within 4Å: Ligands: PLC.3 No protein-ligand interaction detected (PLIP) PLC.15: 11 residues within 4Å: Chain B: R.122, F.125, Y.198, I.202, I.206, L.210, Y.258, I.262, N.311, F.319 Ligands: PLC.16 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.125, B:F.125, B:I.202, B:I.206, B:L.210, B:Y.258, B:I.262 Hydrogen bonds: B:R.122 PLC.16: 1 residues within 4Å: Ligands: PLC.15 No protein-ligand interaction detected (PLIP) PLC.25: 11 residues within 4Å: Chain C: R.122, F.125, Y.198, I.202, I.206, L.210, Y.258, I.262, N.311, F.319 Ligands: PLC.26 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.125, C:I.206, C:L.210, C:Y.258, C:I.262 Hydrogen bonds: C:R.122, C:Y.258 PLC.26: 1 residues within 4Å: Ligands: PLC.25 No protein-ligand interaction detected (PLIP) PLC.36: 10 residues within 4Å: Chain D: R.122, F.125, Y.198, I.202, I.206, L.210, Y.258, N.311, F.319 Ligands: PLC.37 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.125, D:F.125, D:I.202, D:I.206, D:L.210, D:Y.258 Hydrogen bonds: D:R.122, D:Y.258 PLC.37: 1 residues within 4Å: Ligands: PLC.36 No protein-ligand interaction detected (PLIP) PLC.47: 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.48 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.125, E:I.202, E:I.206, E:L.210, E:Y.258 Hydrogen bonds: E:R.122 PLC.48: 1 residues within 4Å: Ligands: PLC.47 No protein-ligand interaction detected (PLIP)

10 x UNL: UNKNOWN LIGAND

UNL.5: 3 residues within 4Å: Chain A: F.271, I.275 Ligands: UNL.50 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.271, A:I.275 UNL.6: 6 residues within 4Å: Chain A: F.214, W.221 Chain B: I.275, V.279, Y.282 Ligands: UNL.17 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.214, A:W.221, A:W.221, B:I.275, B:V.279, B:Y.282 UNL.17: 3 residues within 4Å: Chain B: F.271, I.275 Ligands: UNL.6 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.271, B:I.275 UNL.18: 5 residues within 4Å: Chain B: F.214, W.221 Chain C: I.275, V.279, Y.282 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.275, C:V.279, C:Y.282, B:F.214, B:W.221 UNL.27: 2 residues within 4Å: Chain C: F.271, I.275 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.271, C:I.275 UNL.28: 8 residues within 4Å: Chain C: F.214, T.218, W.221 Chain D: I.275, T.278, V.279, Y.282 Ligands: UNL.38 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.214, C:T.218, C:W.221, D:I.275, D:T.278, D:Y.282, D:Y.282 UNL.38: 3 residues within 4Å: Chain D: F.271, I.275 Ligands: UNL.28 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.271, D:I.275 UNL.39: 6 residues within 4Å: Chain D: F.214, W.221 Chain E: I.275, T.278, Y.282 Ligands: UNL.49 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:I.275, E:Y.282, D:F.214, D:W.221, D:W.221 UNL.49: 3 residues within 4Å: Chain E: F.271, I.275 Ligands: UNL.39 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.271, E:I.275 UNL.50: 7 residues within 4Å: Chain A: I.275, V.279, Y.282 Chain E: F.214, T.218, W.221 Ligands: UNL.5 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:F.214, E:T.218, E:W.221, A:V.279, A:Y.282

12 x BR: BROMIDE ION(Non-covalent)

BR.7: 3 residues within 4Å: Chain A: F.82, A.88, R.89 Ligand excluded by PLIP BR.8: 3 residues within 4Å: Chain A: N.143, R.183, L.184 Ligand excluded by PLIP BR.9: 5 residues within 4Å: Chain A: T.223, Y.225, E.226, H.281, K.284 Ligand excluded by PLIP BR.19: 3 residues within 4Å: Chain B: F.82, A.88, R.89 Ligand excluded by PLIP BR.20: 5 residues within 4Å: Chain B: T.223, Y.225, E.226, H.281, K.284 Ligand excluded by PLIP BR.29: 3 residues within 4Å: Chain C: F.82, A.88, R.89 Ligand excluded by PLIP BR.30: 5 residues within 4Å: Chain C: T.223, Y.225, E.226, H.281, K.284 Ligand excluded by PLIP BR.40: 3 residues within 4Å: Chain D: F.82, A.88, R.89 Ligand excluded by PLIP BR.41: 4 residues within 4Å: Chain D: S.138, N.143, R.183, L.184 Ligand excluded by PLIP BR.42: 5 residues within 4Å: Chain D: T.223, Y.225, E.226, H.281, K.284 Ligand excluded by PLIP BR.51: 2 residues within 4Å: Chain E: F.82, R.89 Ligand excluded by PLIP BR.52: 5 residues within 4Å: Chain E: T.223, Y.225, E.226, H.281, K.284 Ligand excluded by PLIP

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

LMT.10: 5 residues within 4Å: Chain A: F.241, I.244 Chain B: T.248 Ligands: LMT.21, LMT.32 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.241, A:I.244, B:T.248 LMT.21: 5 residues within 4Å: Chain B: F.241, L.245 Chain C: T.248 Ligands: LMT.10, LMT.32 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:T.248, B:F.241, B:L.245 LMT.31: 4 residues within 4Å: Chain C: F.241, I.244 Chain D: T.248 Ligands: LMT.32 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.241, C:I.244, C:I.244, D:T.248 LMT.32: 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.10, LMT.21, LMT.31, LMT.53 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:F.241, C:F.241 LMT.43: 3 residues within 4Å: Chain D: F.241, I.244, L.245 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.241, D:I.244, D:L.245 LMT.53: 3 residues within 4Å: Chain E: F.241, I.244 Ligands: LMT.32 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.241, E:I.244

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

NA.11: 1 residues within 4Å: Chain C: T.230 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.230 NA.12: 5 residues within 4Å: Chain A: V.9, P.72, I.75, W.76, I.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.72, A:I.77 NA.22: 5 residues within 4Å: Chain B: V.9, P.72, I.75, W.76, I.77 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.72, B:I.77 NA.33: 2 residues within 4Å: Chain C: P.72, I.75 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.75 NA.44: 5 residues within 4Å: Chain D: V.9, P.72, I.75, W.76, I.77 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.77 NA.54: 3 residues within 4Å: Chain E: P.72, I.75, I.77 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.75, E:I.77

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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