SMTL ID : 6hpp.1

X-ray structure of GLIC in complex with propionate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-pentamer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: F.78, V.81, R.85 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: N.139, R.179, L.180 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: F.174, A.175 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: R.77, F.78, V.81, R.85 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: F.78, V.81, R.85 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain D: F.78, V.81, R.85 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain E: F.78, V.81, R.85 Ligand excluded by PLIP

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

NA.4: 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.5: 2 residues within 4Å: Chain B: T.226 Chain C: T.226 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.226, C:T.226, C:T.226 NA.12: 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.17: 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:I.71, C:I.73 NA.21: 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:P.68, D:I.73 NA.27: 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.6: 5 residues within 4Å: Ligands: LMT.7, LMT.13, LMT.18, LMT.22, LMT.28 No protein-ligand interaction detected (PLIP) LMT.7: 6 residues within 4Å: Chain A: A.237, I.240 Chain B: T.244 Chain E: A.237 Ligands: LMT.6, LMT.13 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: B:T.244, A:A.237, A:I.240, E:A.237 LMT.13: 7 residues within 4Å: Chain A: A.237 Chain B: A.237, I.240, L.241, T.244 Ligands: LMT.6, LMT.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.237, B:I.240, B:L.241, A:A.237 LMT.18: 5 residues within 4Å: Chain B: A.237 Chain C: A.237, I.240 Ligands: LMT.6, LMT.22 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.237, C:I.240, C:I.240, B:A.237 LMT.22: 4 residues within 4Å: Chain C: A.237 Chain D: A.237 Ligands: LMT.6, LMT.18 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:A.237, D:A.237 LMT.28: 5 residues within 4Å: Chain A: T.244 Chain D: A.237 Chain E: A.237, I.240 Ligands: LMT.6 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: E:A.237, E:I.240, A:T.244, D:A.237

10 x PPI: PROPANOIC ACID(Non-covalent)

PPI.8: 7 residues within 4Å: Chain A: I.25, F.42, R.105 Chain B: R.77, I.131, L.176, E.181 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.25, A:F.42, B:I.131, B:L.176 Salt bridges: A:R.105, B:R.77 Hydrogen bonds: B:E.181 PPI.9: 6 residues within 4Å: Chain A: R.77, I.131, L.176, E.181 Chain E: F.42, R.105 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:L.176 Hydrogen bonds: A:E.181 Salt bridges: A:R.77, E:R.105 PPI.10: 5 residues within 4Å: Chain A: I.73, P.74, I.76, R.85, Y.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.76 Salt bridges: A:R.85 PPI.14: 8 residues within 4Å: Chain B: I.25, F.42, R.105 Chain C: R.77, V.79, I.131, L.176, E.181 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:V.79, C:L.176, B:I.25, B:I.25 Salt bridges: C:R.77, B:R.105 PPI.15: 6 residues within 4Å: Chain B: I.73, P.74, E.75, I.76, R.85, Y.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.76, B:Y.102 Salt bridges: B:R.85 PPI.19: 7 residues within 4Å: Chain C: I.73, P.74, E.75, I.76, R.85, Y.102, E.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.76 Salt bridges: C:R.85 PPI.23: 7 residues within 4Å: Chain C: I.25, F.42, R.105 Chain D: R.77, I.131, L.176, E.181 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.25, C:F.42, D:I.131, D:L.176 Salt bridges: C:R.105, D:R.77 Hydrogen bonds: D:E.181 PPI.24: 8 residues within 4Å: Chain D: I.25, F.42, R.105 Chain E: R.77, V.79, I.131, L.176, E.181 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:V.79, E:I.131, E:L.176, D:F.42 Hydrogen bonds: E:E.181 Salt bridges: E:R.77, D:R.105 PPI.25: 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 PPI.29: 6 residues within 4Å: Chain E: P.74, E.75, I.76, R.85, Y.102, E.104 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.76 Salt bridges: E:R.85

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

2019-10-09

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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