SMTL ID : 6cju.1

Structure of the SthK cyclic nucleotide-gated potassium channel in complex with cAMP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.35 Å

Oligo State

homo-tetramer

Ligands

4 x CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE(Non-covalent)

CMP.1: 7 residues within 4Å: Chain A: F.385, G.386, E.387, M.388, R.396, T.397, A.398 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.386, A:E.387, A:E.387, A:T.397, A:A.398 Salt bridges: A:R.396 CMP.10: 7 residues within 4Å: Chain B: F.385, G.386, E.387, M.388, R.396, T.397, A.398 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.386, B:E.387, B:E.387, B:T.397, B:A.398 Salt bridges: B:R.396 CMP.19: 7 residues within 4Å: Chain C: F.385, G.386, E.387, M.388, R.396, T.397, A.398 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.386, C:E.387, C:E.387, C:T.397, C:A.398 Salt bridges: C:R.396 CMP.28: 7 residues within 4Å: Chain D: F.385, G.386, E.387, M.388, R.396, T.397, A.398 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.386, D:E.387, D:E.387, D:T.397, D:A.398 Salt bridges: D:R.396

32 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)(Non-functional Binders)

PGW.2: 5 residues within 4Å: Chain A: G.186, L.190 Chain B: V.217, V.221 Ligands: PGW.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.221, A:L.190 PGW.3: 1 residues within 4Å: Ligands: PGW.2 No protein-ligand interaction detected (PLIP) PGW.4: 6 residues within 4Å: Chain A: L.51, L.58, L.164, A.185, Y.189 Ligands: PGW.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.58, A:Y.189 PGW.5: 3 residues within 4Å: Chain A: I.47 Ligands: PGW.4, PGW.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.47 PGW.6: 4 residues within 4Å: Chain A: Y.44, I.47, L.58 Ligands: PGW.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.47, A:L.58 PGW.7: 10 residues within 4Å: Chain A: L.53, S.121, L.125, L.128, F.162, G.169, G.173, S.176, L.177 Ligands: PGW.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.53, A:L.125, A:F.162 Hydrogen bonds: A:S.176 PGW.8: 6 residues within 4Å: Chain A: F.162, T.214, Y.218, V.221, L.225 Ligands: PGW.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.162, A:Y.218, A:V.221 PGW.9: 9 residues within 4Å: Chain A: L.156, V.160, T.201, L.240, L.244 Chain B: L.224, A.227, A.228, L.232 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.201, A:L.240, A:L.244, B:L.224, B:A.227 PGW.11: 5 residues within 4Å: Chain B: G.186, L.190 Chain C: V.217, V.221 Ligands: PGW.12 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.221, B:L.190 PGW.12: 1 residues within 4Å: Ligands: PGW.11 No protein-ligand interaction detected (PLIP) PGW.13: 6 residues within 4Å: Chain B: L.51, L.58, L.164, A.185, Y.189 Ligands: PGW.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.58, B:Y.189 PGW.14: 3 residues within 4Å: Chain B: I.47 Ligands: PGW.13, PGW.15 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.47 PGW.15: 4 residues within 4Å: Chain B: Y.44, I.47, L.58 Ligands: PGW.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.47, B:L.58 PGW.16: 10 residues within 4Å: Chain B: L.53, S.121, L.125, L.128, F.162, G.169, G.173, S.176, L.177 Ligands: PGW.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.53, B:L.125, B:F.162 Hydrogen bonds: B:S.176 PGW.17: 6 residues within 4Å: Chain B: F.162, T.214, Y.218, V.221, L.225 Ligands: PGW.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.162, B:Y.218, B:V.221 PGW.18: 9 residues within 4Å: Chain B: L.156, V.160, T.201, L.240, L.244 Chain C: L.224, A.227, A.228, L.232 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:T.201, B:L.240, B:L.244, C:L.224, C:A.227 PGW.20: 5 residues within 4Å: Chain C: G.186, L.190 Chain D: V.217, V.221 Ligands: PGW.21 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.190, D:V.221 PGW.21: 1 residues within 4Å: Ligands: PGW.20 No protein-ligand interaction detected (PLIP) PGW.22: 6 residues within 4Å: Chain C: L.51, L.58, L.164, A.185, Y.189 Ligands: PGW.23 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.58, C:Y.189 PGW.23: 3 residues within 4Å: Chain C: I.47 Ligands: PGW.22, PGW.24 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.47 PGW.24: 4 residues within 4Å: Chain C: Y.44, I.47, L.58 Ligands: PGW.23 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.47, C:L.58 PGW.25: 10 residues within 4Å: Chain C: L.53, S.121, L.125, L.128, F.162, G.169, G.173, S.176, L.177 Ligands: PGW.26 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.53, C:L.125, C:F.162 Hydrogen bonds: C:S.176 PGW.26: 6 residues within 4Å: Chain C: F.162, T.214, Y.218, V.221, L.225 Ligands: PGW.25 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.162, C:Y.218, C:V.221 PGW.27: 9 residues within 4Å: Chain C: L.156, V.160, T.201, L.240, L.244 Chain D: L.224, A.227, A.228, L.232 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:T.201, C:L.240, C:L.244, D:L.224, D:A.227 PGW.29: 5 residues within 4Å: Chain A: V.217, V.221 Chain D: G.186, L.190 Ligands: PGW.30 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.221, D:L.190 PGW.30: 1 residues within 4Å: Ligands: PGW.29 No protein-ligand interaction detected (PLIP) PGW.31: 6 residues within 4Å: Chain D: L.51, L.58, L.164, A.185, Y.189 Ligands: PGW.32 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.58, D:Y.189 PGW.32: 3 residues within 4Å: Chain D: I.47 Ligands: PGW.31, PGW.33 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.47 PGW.33: 4 residues within 4Å: Chain D: Y.44, I.47, L.58 Ligands: PGW.32 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.47, D:L.58 PGW.34: 10 residues within 4Å: Chain D: L.53, S.121, L.125, L.128, F.162, G.169, G.173, S.176, L.177 Ligands: PGW.35 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.53, D:L.125, D:F.162 Hydrogen bonds: D:S.176 PGW.35: 6 residues within 4Å: Chain D: F.162, T.214, Y.218, V.221, L.225 Ligands: PGW.34 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.162, D:Y.218, D:V.221 PGW.36: 9 residues within 4Å: Chain A: L.224, A.227, A.228, L.232 Chain D: L.156, V.160, T.201, L.240, L.244 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:T.201, D:L.240, D:L.244, A:L.224, A:A.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rheinberger, J. et al., Ligand discrimination and gating in cyclic nucleotide-gated ion channels from apo and partial agonist-bound cryo-EM structures. Elife (2018)

Release Date

2018-08-01

Peptides

SthK cyclic nucleotide-gated potassium channel: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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SthK cyclic nucleotide-gated potassium channel

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