SMTL ID : 6fvs.1

The active form of a pentameric ion channel (sTeLIC) gated by alkaline pH - sTeLIC in complex with Barium ions (Ba2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-pentamer

Ligands

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

BNG.1: 13 residues within 4Å: Chain A: V.212, S.213, T.216, K.224, D.227, L.228, G.231, N.232 Chain B: I.226, D.227, G.230, G.231, L.234 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.212, A:T.216, A:L.228, A:L.228, B:I.226, B:L.234, B:L.234 Hydrogen bonds: A:K.224, A:G.231 Water bridges: A:D.227 Salt bridges: A:K.224 BNG.2: 13 residues within 4Å: Chain B: V.212, S.213, T.216, K.224, D.227, L.228, G.231, N.232 Chain C: I.226, D.227, G.230, G.231, L.234 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:V.212, B:T.216, B:L.228, B:L.228, C:I.226, C:L.234, C:L.234 Hydrogen bonds: B:K.224, B:G.231 Salt bridges: B:K.224 BNG.4: 15 residues within 4Å: Chain C: V.212, S.213, T.216, K.224, D.227, L.228, G.231, N.232, L.235 Chain D: I.226, D.227, G.230, G.231, L.234 Ligands: BNG.7 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.212, C:T.216, C:L.228, C:L.228, D:I.226, D:L.234, D:L.234 Hydrogen bonds: C:K.224 Salt bridges: C:K.224 BNG.7: 16 residues within 4Å: Chain D: V.212, S.213, T.216, K.224, D.227, L.228, G.231, N.232, L.235 Chain E: I.226, D.227, G.230, G.231, L.234 Ligands: BNG.4, BNG.8 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:V.212, D:T.216, D:L.228, D:L.228, E:I.226, E:L.234, E:L.234 Hydrogen bonds: D:K.224, D:G.231 Salt bridges: D:K.224 BNG.8: 14 residues within 4Å: Chain A: I.226, D.227, G.230, G.231, L.234 Chain E: V.212, S.213, T.216, K.224, D.227, L.228, G.231, N.232 Ligands: BNG.7 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain E Hydrophobic interactions: A:I.226, A:L.234, A:L.234, E:V.212, E:T.216, E:L.228, E:L.228 Water bridges: A:D.227, A:D.227 Hydrogen bonds: E:K.224, E:G.231 Salt bridges: E:K.224

2 x BA: BARIUM ION(Non-functional Binders)

BA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) BA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 2 residues within 4Å: Chain D: H.49, E.98 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.49, D:E.98, D:E.98

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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