SMTL ID : 4qh5.1

The GLIC pentameric Ligand-Gated Ion Channel (wild-type) crystallized in phosphate buffer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-pentamer

Ligands

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

LMT.1: 3 residues within 4Å: Ligands: LMT.2, LMT.8, LMT.15 No protein-ligand interaction detected (PLIP) LMT.2: 8 residues within 4Å: Chain A: A.236, I.239, L.240, T.243 Chain B: T.243 Chain E: A.236 Ligands: LMT.1, LMT.15 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: B:T.243, A:A.236, A:I.239, A:L.240, E:A.236 LMT.4: 5 residues within 4Å: Chain A: A.236 Chain B: A.236, I.239, L.240 Chain C: T.243 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:A.236, B:I.239, B:L.240, A:A.236, C:T.243 LMT.8: 4 residues within 4Å: Chain B: A.236 Chain C: I.239, L.240 Ligands: LMT.1 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.239, C:I.239, C:L.240, B:A.236 LMT.12: 5 residues within 4Å: Chain D: I.235, A.236, I.239, L.240 Chain E: T.243 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:T.243, D:I.235, D:I.239, D:L.240 LMT.15: 6 residues within 4Å: Chain A: T.243 Chain D: A.236 Chain E: A.236, I.239 Ligands: LMT.1, LMT.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:T.243, E:A.236, E:I.239

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

CL.3: 3 residues within 4Å: Chain A: P.73, I.75, R.76 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: P.73, I.75, R.76, R.84 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain C: P.73, I.75, R.84 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain D: P.73, I.75, R.76 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain E: P.73, I.75, R.76 Ligand excluded by PLIP

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

NA.6: 3 residues within 4Å: Chain B: P.67, I.70, I.72 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.72 NA.7: 3 residues within 4Å: Chain C: T.225 Chain D: T.225 Chain E: T.225 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: B:T.225, C:T.225, D:T.225, A:T.225 NA.10: 4 residues within 4Å: Chain C: P.67, E.68, I.70, I.72 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.70, C:I.72 NA.13: 4 residues within 4Å: Chain D: P.67, I.70, W.71, I.72 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.72

2 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.11: 7 residues within 4Å: Chain C: R.117, F.120, Y.193, I.201, Y.253, N.306, F.314 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.120, C:F.120, C:Y.193, C:I.201, C:Y.253 Hydrogen bonds: C:R.117 PLC.17: 10 residues within 4Å: Chain E: R.117, F.120, Y.193, I.197, I.201, L.205, Y.253, I.257, N.306, F.314 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.120, E:F.120, E:F.120, E:Y.193, E:I.197, E:I.201, E:L.205, E:Y.253, E:I.257 Hydrogen bonds: E:R.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fourati, Z. et al., Structural characterization of potential modulation sites in the extracellular domain of the prokaryotic pentameric proton-gated ion channel GLIC. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-03-11

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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