SMTL ID : 6fl9.1

The active form of a pentameric ion channel (sTeLIC) gated by alkaline pH - Wild type 2.3 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-pentamer

Ligands

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 6 residues within 4Å: Chain A: L.61, L.65, W.75, R.92 Chain E: T.60, R.92 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.92 PG4.2: 7 residues within 4Å: Chain A: T.60, N.91, R.92, L.93 Chain B: L.61, F.78, R.92 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.78, B:R.92, A:N.91 Water bridges: B:R.92, B:R.92 PG4.5: 9 residues within 4Å: Chain B: T.60, N.91, R.92 Chain C: L.61, L.65, W.75, A.77, F.78, R.92 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:F.78, C:F.78, C:R.92, B:R.92 PG4.6: 7 residues within 4Å: Chain C: N.91, R.92 Chain D: L.61, L.65, W.75, A.77, R.92 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.91, C:R.92, D:F.78, D:R.92 PG4.9: 6 residues within 4Å: Chain D: T.60, R.92 Chain E: L.61, L.65, F.78, R.92 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.92

5 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.3: 14 residues within 4Å: Chain A: V.212, S.213, T.216, D.227, L.228, G.231, N.232, L.235 Chain B: I.226, D.227, G.230, G.231, L.234 Ligands: BNG.10 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.212, A:T.216, A:L.235, B:L.234, B:L.234 Hydrogen bonds: A:G.231 BNG.4: 12 residues within 4Å: Chain B: V.212, S.213, T.216, D.227, L.228, G.231, N.232 Chain C: I.226, D.227, G.230, G.231, L.234 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:V.212, B:T.216, B:L.228, C:I.226, C:L.234 Hydrogen bonds: B:D.227 BNG.7: 13 residues within 4Å: Chain C: V.212, S.213, T.216, D.227, L.228, G.231, N.232 Chain D: I.226, D.227, G.230, G.231, L.234 Ligands: BNG.8 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.212, C:T.216, D:I.226, D:L.234 Hydrogen bonds: C:D.227, C:G.231 Water bridges: C:K.224 BNG.8: 13 residues within 4Å: Chain D: V.212, S.213, T.216, D.227, L.228, G.231, N.232 Chain E: I.226, D.227, G.230, G.231, L.234 Ligands: BNG.7 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:V.212, D:T.216, D:L.228, E:I.226, E:L.234 BNG.10: 14 residues within 4Å: Chain A: I.226, D.227, G.230, G.231, L.234 Chain E: V.212, S.213, T.216, D.227, L.228, G.231, N.232, L.235 Ligands: BNG.3 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:V.212, E:T.216, A:I.226, A:L.234 Hydrogen bonds: E:N.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, H. et al., Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-05-16

Peptides

Cys-loop ligand-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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Cys-loop ligand-gated ion channel

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