SMTL ID : 6hj3.1

Xray structure of GLIC in complex with fumarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-pentamer

Ligands

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

PLC.1: 7 residues within 4Å: Chain A: R.118, F.121, Y.194, Y.254, N.307, F.315 Ligands: PLC.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.121, A:F.121, A:F.121, A:Y.194, A:Y.254 Hydrogen bonds: A:R.118 PLC.2: 8 residues within 4Å: Chain A: F.210, W.213, T.214, W.217 Chain B: F.267, T.274, V.275, Y.278 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.267, B:T.274, B:V.275, B:Y.278, A:F.210, A:W.213, A:W.213, A:T.214, A:W.217, A:W.217 PLC.3: 1 residues within 4Å: Ligands: PLC.1 No protein-ligand interaction detected (PLIP) PLC.9: 7 residues within 4Å: Chain A: F.267, I.271, V.275, Y.278 Chain E: F.210, T.214, W.217 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:T.214, E:W.217, E:W.217, E:W.217, A:F.267, A:I.271, A:V.275, A:Y.278 PLC.14: 9 residues within 4Å: Chain B: R.118, F.121, Y.194, I.198, 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:F.121, B:Y.194, B:I.198, B:Y.254, B:I.258 Hydrogen bonds: B:R.118 PLC.15: 8 residues within 4Å: Chain B: F.210, W.213, T.214, W.217 Chain C: I.271, T.274, V.275, Y.278 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:F.210, B:F.210, B:W.213, B:T.214, B:W.217, C:I.271, C:I.271, C:T.274, C:V.275, C:Y.278 PLC.16: 1 residues within 4Å: Ligands: PLC.14 No protein-ligand interaction detected (PLIP) PLC.21: 9 residues within 4Å: Chain C: R.118, F.121, Y.194, I.198, Y.254, I.258, N.307, F.315 Ligands: PLC.23 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.121, C:Y.194, C:I.198, C:I.258 Hydrogen bonds: C:Y.194 PLC.22: 8 residues within 4Å: Chain C: W.213, T.214, W.217 Chain D: F.267, I.271, T.274, V.275, Y.278 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:F.267, D:T.274, D:V.275, D:Y.278, C:W.213, C:T.214, C:W.217, C:W.217, C:W.217 PLC.23: 1 residues within 4Å: Ligands: PLC.21 No protein-ligand interaction detected (PLIP) PLC.30: 7 residues within 4Å: Chain D: R.118, F.121, Y.194, Y.254, N.307, F.315 Ligands: PLC.31 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.121, D:Y.194, D:Y.254 Salt bridges: D:R.118 PLC.31: 1 residues within 4Å: Ligands: PLC.30 No protein-ligand interaction detected (PLIP) PLC.37: 8 residues within 4Å: Chain D: F.210, W.213, T.214, W.217 Chain E: I.271, T.274, V.275, Y.278 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:F.210, D:W.213, D:W.217, D:W.217, D:W.217, E:I.271, E:I.271, E:T.274, E:Y.278, E:Y.278 PLC.38: 9 residues within 4Å: Chain E: R.118, F.121, Y.194, I.202, L.206, Y.254, N.307, F.315 Ligands: PLC.39 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.121, E:F.121, E:F.121, E:Y.194, E:I.202, E:L.206, E:Y.254 Hydrogen bonds: E:R.118 PLC.39: 1 residues within 4Å: Ligands: PLC.38 No protein-ligand interaction detected (PLIP)

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

CL.4: 4 residues within 4Å: Chain A: R.77, F.78, A.84, R.85 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: N.139, D.178, R.179, L.180 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: A.175 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: P.74, I.76, R.85 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: R.77, F.78, A.84, R.85 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: P.74, I.76, R.85 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain C: R.77, F.78, A.84, R.85 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain C: P.74, R.85 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain D: R.77, F.78, A.84, R.85 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain D: P.74, I.76, R.85 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain E: R.77, F.78, A.84, R.85 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain E: P.74, I.76, R.85 Ligand excluded by PLIP

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

NA.7: 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.13: 3 residues within 4Å: Chain B: T.226 Chain C: T.226 Chain D: T.226 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:T.226, C:T.226, B:T.226 Water bridges: E:T.226 NA.18: 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:I.71, B:I.73 NA.25: 3 residues within 4Å: Chain C: P.68, I.71, I.73 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.71, C:I.73 NA.33: 4 residues within 4Å: Chain D: 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.41: 3 residues within 4Å: Chain E: P.68, I.71, 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-covalent)(Non-functional Binders)

LMT.8: 8 residues within 4Å: Chain A: A.237, I.240, L.241, T.244 Chain B: I.240 Chain E: A.237 Ligands: LMT.19, LMT.29 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: A:I.240, A:L.241, B:I.240, E:A.237 LMT.19: 5 residues within 4Å: Chain A: A.237 Chain B: A.237, I.240 Ligands: LMT.8, LMT.29 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.240, B:I.240, A:A.237 LMT.26: 5 residues within 4Å: Chain B: A.237 Chain C: A.237, I.240, T.244 Ligands: LMT.29 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:A.237, C:I.240, C:I.240 LMT.29: 5 residues within 4Å: Ligands: LMT.8, LMT.19, LMT.26, LMT.34, LMT.42 No protein-ligand interaction detected (PLIP) LMT.34: 8 residues within 4Å: Chain C: A.237 Chain D: I.233, A.237, I.240, L.241, T.244 Ligands: LMT.29, LMT.42 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:A.237, D:I.233, D:A.237, D:I.240, D:L.241 LMT.42: 6 residues within 4Å: Chain D: A.237 Chain E: A.237, I.240, T.244 Ligands: LMT.29, LMT.34 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:I.240, E:I.240, D:A.237

5 x FUM: FUMARIC ACID(Non-covalent)

FUM.11: 10 residues within 4Å: Chain A: R.77, V.79, I.131, F.174, L.176, E.181 Chain E: I.25, F.42, R.105, N.152 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:I.131, E:F.42 Hydrogen bonds: A:E.181, E:N.152 Salt bridges: A:R.77, E:R.105 FUM.12: 10 residues within 4Å: Chain A: I.25, F.42, R.105, N.152 Chain B: R.77, V.79, I.131, F.174, L.176, E.181 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.131, A:F.42 Hydrogen bonds: B:E.181, B:E.181, B:E.181, A:N.152 Salt bridges: B:R.77, A:R.105 FUM.27: 10 residues within 4Å: Chain B: I.25, F.42, R.105, N.152 Chain C: R.77, V.79, I.131, F.174, L.176, E.181 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.42, C:I.131 Hydrogen bonds: B:N.152, C:E.181 Salt bridges: B:R.105, C:R.77 FUM.35: 10 residues within 4Å: Chain C: I.25, F.42, R.105, N.152 Chain D: R.77, V.79, I.131, F.174, L.176, E.181 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.131, D:L.176, C:F.42 Hydrogen bonds: D:E.181, C:N.152 Salt bridges: D:R.77, C:R.105 FUM.44: 10 residues within 4Å: Chain D: I.25, F.42, R.105, N.152 Chain E: R.77, V.79, I.131, F.174, L.176, E.181 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:I.131, D:F.42 Salt bridges: E:R.77, D:R.105 Hydrogen bonds: D:N.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fourati, Z. et al., Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel. Acta Crystallogr D Struct Biol (2020)

Release Date

2019-09-11

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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