SMTL ID : 6wek.1

Structure of cGMP-bound WT TAX-4 reconstituted in lipid nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x PCG: CYCLIC GUANOSINE MONOPHOSPHATE(Covalent)

PCG.1: 10 residues within 4Å: Chain A: C.521, F.558, G.559, E.560, L.561, S.562, R.575, T.576, A.577, V.579 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.559, A:E.560, A:L.561, A:S.562, A:S.562, A:T.576, A:A.577 Salt bridges: A:R.575 PCG.9: 10 residues within 4Å: Chain B: C.521, F.558, G.559, E.560, L.561, S.562, R.575, T.576, A.577, V.579 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.559, B:E.560, B:L.561, B:S.562, B:S.562, B:T.576, B:A.577 Salt bridges: B:R.575 PCG.17: 10 residues within 4Å: Chain C: C.521, F.558, G.559, E.560, L.561, S.562, R.575, T.576, A.577, V.579 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.559, C:E.560, C:L.561, C:S.562, C:S.562, C:T.576, C:A.577 Salt bridges: C:R.575 PCG.25: 10 residues within 4Å: Chain D: C.521, F.558, G.559, E.560, L.561, S.562, R.575, T.576, A.577, V.579 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.559, D:E.560, D:L.561, D:S.562, D:S.562, D:T.576, D:A.577 Salt bridges: D:R.575

24 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.2: 11 residues within 4Å: Chain A: Y.134, D.147, L.148, C.172, Y.174, Y.197, F.200, W.204, F.207, L.359 Ligands: CPL.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.134, A:F.200, A:F.200, A:W.204, A:W.204, A:F.207 Hydrogen bonds: A:Y.197 Salt bridges: A:E.171 pi-Cation interactions: A:Y.174 CPL.3: 3 residues within 4Å: Chain A: W.333, I.387, L.394 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.333, A:L.394 CPL.4: 3 residues within 4Å: Chain A: L.326, W.329, I.330 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.326, A:W.329, A:W.329 CPL.5: 8 residues within 4Å: Chain A: Y.132, I.133, L.136, V.290, L.294, W.314, Y.315, I.318 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.132, A:I.133, A:L.136, A:V.290, A:L.294, A:W.314, A:W.314, A:I.318 CPL.6: 4 residues within 4Å: Chain A: Y.315, I.318, W.322, L.326 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.315, A:W.322, A:W.322, A:L.326 CPL.8: 7 residues within 4Å: Chain A: V.317, H.321, T.358, L.359, L.360, Y.363 Ligands: CPL.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.317, A:L.359, A:L.360, A:Y.363, A:Y.363 CPL.10: 10 residues within 4Å: Chain B: Y.134, D.147, L.148, C.172, Y.174, Y.197, F.200, W.204, F.207 Ligands: CPL.16 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.134, B:F.200, B:W.204, B:W.204, B:F.207 Hydrogen bonds: B:Y.197 pi-Cation interactions: B:Y.174 CPL.11: 3 residues within 4Å: Chain B: W.333, I.387, L.394 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.333, B:L.394 CPL.12: 4 residues within 4Å: Chain B: L.326, W.329, I.330, W.333 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.326, B:W.329, B:W.329, B:I.330, B:W.333 CPL.13: 8 residues within 4Å: Chain B: Y.132, I.133, L.136, V.290, L.294, W.314, Y.315, I.318 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.132, B:L.136, B:L.294, B:W.314, B:W.314, B:Y.315, B:I.318 CPL.14: 4 residues within 4Å: Chain B: Y.315, I.318, W.322, L.326 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.315, B:W.322, B:W.322, B:L.326 CPL.16: 7 residues within 4Å: Chain B: V.317, H.321, T.358, L.359, L.360, Y.363 Ligands: CPL.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.317, B:L.359, B:L.360, B:Y.363, B:Y.363 CPL.18: 10 residues within 4Å: Chain C: Y.134, D.147, L.148, C.172, Y.174, Y.197, F.200, W.204, F.207 Ligands: CPL.24 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.134, C:F.200, C:W.204, C:W.204, C:F.207 Hydrogen bonds: C:Y.197 pi-Cation interactions: C:Y.174 CPL.19: 3 residues within 4Å: Chain C: W.333, I.387, L.394 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.333, C:L.394 CPL.20: 4 residues within 4Å: Chain C: L.326, W.329, I.330, W.333 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.326, C:W.329, C:W.329, C:I.330, C:W.333 CPL.21: 8 residues within 4Å: Chain C: Y.132, I.133, L.136, V.290, L.294, W.314, Y.315, I.318 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.132, C:L.136, C:L.294, C:W.314, C:W.314, C:Y.315, C:I.318 CPL.22: 4 residues within 4Å: Chain C: Y.315, I.318, W.322, L.326 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.315, C:W.322, C:W.322, C:L.326 CPL.24: 7 residues within 4Å: Chain C: V.317, H.321, T.358, L.359, L.360, Y.363 Ligands: CPL.18 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.317, C:L.359, C:L.360, C:Y.363, C:Y.363 CPL.26: 10 residues within 4Å: Chain D: Y.134, D.147, L.148, C.172, Y.174, Y.197, F.200, W.204, F.207 Ligands: CPL.32 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.134, D:F.200, D:W.204, D:W.204, D:F.207 Hydrogen bonds: D:Y.197 pi-Cation interactions: D:Y.174 CPL.27: 3 residues within 4Å: Chain D: W.333, I.387, L.394 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.333, D:L.394 CPL.28: 4 residues within 4Å: Chain D: L.326, W.329, I.330, W.333 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.326, D:W.329, D:W.329, D:I.330, D:W.333 CPL.29: 8 residues within 4Å: Chain D: Y.132, I.133, L.136, V.290, L.294, W.314, Y.315, I.318 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.132, D:L.136, D:L.294, D:W.314, D:W.314, D:Y.315, D:I.318 CPL.30: 4 residues within 4Å: Chain D: Y.315, I.318, W.322, L.326 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.315, D:W.322, D:W.322, D:L.326 CPL.32: 7 residues within 4Å: Chain D: V.317, H.321, T.358, L.359, L.360, Y.363 Ligands: CPL.26 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.317, D:L.359, D:L.360, D:Y.363, D:Y.363

4 x PX2: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX2.7: 3 residues within 4Å: Chain A: W.333, R.385, N.386 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.386 Salt bridges: A:R.385 PX2.15: 5 residues within 4Å: Chain B: W.333, R.385, N.386, I.387, A.390 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.386, B:I.387, B:A.390 Salt bridges: B:R.385 PX2.23: 5 residues within 4Å: Chain C: W.333, R.385, N.386, I.387, A.390 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:N.386, C:I.387, C:A.390 Salt bridges: C:R.385 PX2.31: 5 residues within 4Å: Chain D: W.333, R.385, N.386, I.387, A.390 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:N.386, D:I.387, D:A.390 Salt bridges: D:R.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Mechanism of ligand activation of a eukaryotic cyclic nucleotide-gated channel. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-06-03

Peptides

Cyclic nucleotide-gated cation 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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Cyclic nucleotide-gated cation channel

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