SMTL ID : 6vxz.1

SthK P300A cyclic nucleotide-gated potassium channel in the closed state, in complex with cAMP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.42 Å

Oligo State

homo-tetramer

Ligands

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

CMP.1: 7 residues within 4Å: Chain A: Y.376, G.386, E.387, M.388, A.389, R.396, T.397 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.386, A:E.387, A:M.388, A:A.389, A:T.397 Salt bridges: A:R.396 CMP.8: 7 residues within 4Å: Chain B: Y.376, G.386, E.387, M.388, A.389, R.396, T.397 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.386, B:E.387, B:M.388, B:A.389, B:T.397 Salt bridges: B:R.396 CMP.15: 7 residues within 4Å: Chain C: Y.376, G.386, E.387, M.388, A.389, R.396, T.397 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.386, C:E.387, C:M.388, C:A.389, C:T.397 Salt bridges: C:R.396 CMP.22: 7 residues within 4Å: Chain D: Y.376, G.386, E.387, M.388, A.389, R.396, T.397 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.386, D:E.387, D:M.388, D:A.389, D:T.397 Salt bridges: D:R.396

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

PGW.2: 4 residues within 4Å: Chain A: G.186, Y.189 Chain B: P.213 Ligands: PGW.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.189 PGW.3: 8 residues within 4Å: Chain A: L.51, F.55, S.57, L.164, A.185, Y.189 Ligands: PGW.2, PGW.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.51, A:L.164 PGW.4: 7 residues within 4Å: Chain A: L.53, S.121, S.124, L.128, G.169, S.176, L.177 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.53, A:L.128, A:L.177 Hydrogen bonds: A:S.124 PGW.5: 11 residues within 4Å: Chain A: V.160, L.200, Y.230, L.240 Chain B: R.155, F.162, L.225, A.227, A.228, L.232 Ligands: PGW.6 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.230, A:L.240, B:F.162, B:L.225, B:A.227, B:L.232 Salt bridges: B:R.155 PGW.6: 8 residues within 4Å: Chain A: N.150, L.153, L.157, K.243, L.244 Chain D: R.252, E.256 Ligands: PGW.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.153, A:L.157 Hydrogen bonds: A:N.150, D:E.256 Salt bridges: D:R.252 PGW.7: 4 residues within 4Å: Chain A: Y.44, I.47, R.48 Ligands: PGW.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.47 PGW.9: 4 residues within 4Å: Chain B: G.186, Y.189 Chain C: P.213 Ligands: PGW.10 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.189 PGW.10: 8 residues within 4Å: Chain B: L.51, F.55, S.57, L.164, A.185, Y.189 Ligands: PGW.9, PGW.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.51, B:L.164 PGW.11: 7 residues within 4Å: Chain B: L.53, S.121, S.124, L.128, G.169, S.176, L.177 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.53, B:L.128, B:L.177 Hydrogen bonds: B:S.124 PGW.12: 11 residues within 4Å: Chain B: V.160, L.200, Y.230, L.240 Chain C: R.155, F.162, L.225, A.227, A.228, L.232 Ligands: PGW.13 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.162, C:L.225, C:A.227, C:A.228, C:L.232, B:Y.230, B:L.240 Salt bridges: C:R.155 PGW.13: 8 residues within 4Å: Chain A: R.252, E.256 Chain B: N.150, L.153, L.157, K.243, L.244 Ligands: PGW.12 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.153, B:L.157 Hydrogen bonds: B:N.150, A:E.256 Salt bridges: A:R.252 PGW.14: 4 residues within 4Å: Chain B: Y.44, I.47, R.48 Ligands: PGW.10 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.47 PGW.16: 4 residues within 4Å: Chain C: G.186, Y.189 Chain D: P.213 Ligands: PGW.17 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.189 PGW.17: 8 residues within 4Å: Chain C: L.51, F.55, S.57, L.164, A.185, Y.189 Ligands: PGW.16, PGW.21 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.51, C:L.164 PGW.18: 7 residues within 4Å: Chain C: L.53, S.121, S.124, L.128, G.169, S.176, L.177 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.53, C:L.128, C:L.177 Hydrogen bonds: C:S.124 PGW.19: 11 residues within 4Å: Chain C: V.160, L.200, Y.230, L.240 Chain D: R.155, F.162, L.225, A.227, A.228, L.232 Ligands: PGW.20 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.162, D:L.225, D:A.227, D:A.228, D:L.232, C:Y.230, C:L.240 Salt bridges: D:R.155 PGW.20: 8 residues within 4Å: Chain B: R.252, E.256 Chain C: N.150, L.153, L.157, K.243, L.244 Ligands: PGW.19 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.153, C:L.157 Hydrogen bonds: C:N.150, B:E.256 Salt bridges: B:R.252 PGW.21: 4 residues within 4Å: Chain C: Y.44, I.47, R.48 Ligands: PGW.17 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.47 PGW.23: 4 residues within 4Å: Chain A: P.213 Chain D: G.186, Y.189 Ligands: PGW.24 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.189 PGW.24: 8 residues within 4Å: Chain D: L.51, F.55, S.57, L.164, A.185, Y.189 Ligands: PGW.23, PGW.28 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.51, D:L.164 PGW.25: 7 residues within 4Å: Chain D: L.53, S.121, S.124, L.128, G.169, S.176, L.177 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.53, D:L.128, D:L.177 Hydrogen bonds: D:S.124 PGW.26: 11 residues within 4Å: Chain A: R.155, F.162, L.225, A.227, A.228, L.232 Chain D: V.160, L.200, Y.230, L.240 Ligands: PGW.27 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.162, A:L.225, A:A.227, A:A.228, A:L.232, D:Y.230, D:L.240 Salt bridges: A:R.155 PGW.27: 8 residues within 4Å: Chain C: R.252, E.256 Chain D: N.150, L.153, L.157, K.243, L.244 Ligands: PGW.26 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.153, D:L.157 Hydrogen bonds: D:N.150, C:E.256 Salt bridges: C:R.252 PGW.28: 4 residues within 4Å: Chain D: Y.44, I.47, R.48 Ligands: PGW.24 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidpeter, P.A.M. et al., Prolyl isomerization controls activation kinetics of a cyclic nucleotide-gated ion channel. Nat Commun (2020)

Release Date

2020-11-11

Peptides

SthK: 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

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