SMTL ID : 6hji.1

Xray structure of GLIC in complex with crotonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-pentamer

Ligands

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

PLC.1: 8 residues within 4Å: Chain A: R.118, F.121, I.198, I.202, 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:I.198, A:I.202, A:Y.254 Hydrogen bonds: A:R.118 PLC.2: 7 residues within 4Å: Chain A: W.213, T.214, W.217 Chain B: F.267, I.271, V.275, Y.278 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.267, B:I.271, B:Y.278, A:W.213, A:T.214, A:W.217, A:W.217, A:W.217 PLC.3: 1 residues within 4Å: Ligands: PLC.1 No protein-ligand interaction detected (PLIP) PLC.12: 10 residues within 4Å: Chain B: R.118, F.121, Y.194, I.198, I.202, Y.254, I.258, N.307, F.315 Ligands: PLC.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.121, B:F.121, B:Y.194, B:I.198, B:Y.254, B:I.258 Hydrogen bonds: B:R.118 PLC.13: 7 residues within 4Å: Chain B: W.213, T.214, W.217 Chain C: F.267, I.271, V.275, Y.278 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:W.213, B:T.214, B:W.217, B:W.217, C:F.267, C:I.271, C:V.275, C:Y.278 PLC.14: 1 residues within 4Å: Ligands: PLC.12 No protein-ligand interaction detected (PLIP) PLC.21: 9 residues within 4Å: Chain C: R.118, F.121, Y.194, I.202, L.206, Y.254, N.307, F.315 Ligands: PLC.23 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.121, C:F.121, C:F.121, C:Y.194, C:I.202, C:L.206, C:Y.254 Hydrogen bonds: C:R.118 PLC.22: 6 residues within 4Å: Chain C: W.213, T.214, W.217 Chain D: I.271, V.275, Y.278 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.213, C:T.214, C:W.217, C:W.217, D:I.271, D:V.275, D:Y.278 PLC.23: 1 residues within 4Å: Ligands: PLC.21 No protein-ligand interaction detected (PLIP) PLC.28: 10 residues within 4Å: Chain D: R.118, F.121, Y.194, I.198, I.202, L.203, Y.254, N.307, F.315 Ligands: PLC.30 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.121, D:F.121, D:Y.194, D:I.198, D:I.202, D:L.203 Hydrogen bonds: D:R.118 PLC.29: 6 residues within 4Å: Chain D: W.213, T.214, W.217 Chain E: I.271, V.275, Y.278 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:W.213, D:T.214, D:W.217, E:V.275, E:Y.278 PLC.30: 1 residues within 4Å: Ligands: PLC.28 No protein-ligand interaction detected (PLIP) PLC.37: 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 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.121, E:F.121, E:Y.194, E:I.202, E:L.206, E:Y.254 Hydrogen bonds: E:R.118 PLC.38: 7 residues within 4Å: Chain A: F.267, I.271, V.275, Y.278 Chain E: W.213, T.214, W.217 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: A:F.267, A:I.271, A:V.275, A:Y.278, E:W.213, E:T.214, E:W.217, E:W.217 PLC.39: 1 residues within 4Å: Ligands: PLC.37 No protein-ligand interaction detected (PLIP)

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

CL.4: 3 residues within 4Å: Chain A: F.78, A.84, R.85 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: N.139, R.179, L.180 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: A.175 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: P.74, R.85 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: F.78, V.81, 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: 3 residues within 4Å: Chain C: F.78, V.81, R.85 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain C: P.74, R.85 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain D: F.78, V.81, 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: 3 residues within 4Å: Chain E: F.78, V.81, R.85 Ligand excluded by PLIP CL.44: 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.8: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.226 NA.16: 3 residues within 4Å: Chain B: P.68, I.71, I.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.68, 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.32: 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:P.68, 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:P.68, E:I.73

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

LMT.9: 5 residues within 4Å: Ligands: LMT.10, LMT.17, LMT.26, LMT.33, LMT.42 No protein-ligand interaction detected (PLIP) LMT.10: 6 residues within 4Å: Chain A: A.237, I.240, L.241 Chain B: T.244 Chain E: A.237 Ligands: LMT.9 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: E:A.237, B:T.244, A:A.237, A:I.240, A:L.241 LMT.17: 5 residues within 4Å: Chain B: A.237, I.240, L.241 Chain C: T.244 Ligands: LMT.9 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.237, B:I.240, B:I.240, B:L.241, C:T.244 LMT.26: 6 residues within 4Å: Chain B: A.237 Chain C: A.237, I.240 Chain D: T.244 Ligands: LMT.9, LMT.33 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: D:T.244, B:A.237, C:A.237, C:I.240, C:I.240 LMT.33: 8 residues within 4Å: Chain C: A.237 Chain D: I.233, A.237, I.240, L.241 Chain E: T.244 Ligands: LMT.9, LMT.26 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: D:A.237, D:I.240, D:I.240, E:T.244, C:A.237 LMT.42: 9 residues within 4Å: Chain A: T.244 Chain D: A.237 Chain E: I.233, I.236, A.237, I.240, L.241, T.244 Ligands: LMT.9 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: D:A.237, A:T.244, E:I.236, E:A.237, E:I.240, E:L.241

5 x BEO: BUTENOIC ACID(Non-covalent)

BEO.18: 7 residues within 4Å: Chain A: I.25, F.42, R.105, N.152 Chain B: I.131, L.176, E.181 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.25, B:I.131, B:L.176 Salt bridges: A:R.105, B:R.77 BEO.19: 7 residues within 4Å: Chain B: F.42, R.105 Chain C: R.77, V.79, I.131, L.176, E.181 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.79, B:F.42 Salt bridges: C:R.77, B:R.105 BEO.34: 7 residues within 4Å: Chain C: I.25, F.42, R.105 Chain D: R.77, I.131, L.176, E.181 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.25, C:F.42, D:L.176 Salt bridges: C:R.105, D:R.77 Hydrogen bonds: D:E.181 BEO.35: 6 residues within 4Å: Chain D: F.42, R.105 Chain E: R.77, I.131, L.176, E.181 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.42, E:L.176 Salt bridges: D:R.105, E:R.77 Hydrogen bonds: E:E.181 BEO.43: 6 residues within 4Å: Chain A: R.77, I.131, L.176, E.181 Chain E: F.42, R.105 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:E.181 Salt bridges: A:R.77, E:R.105 Hydrophobic interactions: E:F.42

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

2019-09-18

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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