SMTL ID : 6gyo.1

Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel in complex with cAMP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

CMP.1: 13 residues within 4Å: Chain A: V.444, T.452, F.460, G.461, E.462, I.463, C.464, R.471, T.472, A.473, R.512, R.515, I.516 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.452, A:G.461, A:E.462, A:E.462, A:I.463, A:C.464, A:T.472, A:R.512, A:R.515 Salt bridges: A:R.471 CMP.16: 13 residues within 4Å: Chain B: V.444, T.452, F.460, G.461, E.462, I.463, C.464, R.471, T.472, A.473, R.512, R.515, I.516 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.452, B:G.461, B:E.462, B:E.462, B:I.463, B:C.464, B:T.472, B:R.512, B:R.515 Salt bridges: B:R.471 CMP.28: 13 residues within 4Å: Chain C: V.444, T.452, F.460, G.461, E.462, I.463, C.464, R.471, T.472, A.473, R.512, R.515, I.516 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.452, C:G.461, C:E.462, C:E.462, C:I.463, C:C.464, C:T.472, C:R.512, C:R.515 Salt bridges: C:R.471 CMP.41: 13 residues within 4Å: Chain D: V.444, T.452, F.460, G.461, E.462, I.463, C.464, R.471, T.472, A.473, R.512, R.515, I.516 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:T.452, D:G.461, D:E.462, D:E.462, D:I.463, D:C.464, D:T.472, D:R.512, D:R.515 Salt bridges: D:R.471

28 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.2: 11 residues within 4Å: Chain A: W.143, L.187, L.190, L.193, S.194, I.197, R.198, W.233 Ligands: PC1.5, PC1.10, PC1.11 Ligand excluded by PLIP PC1.3: 8 residues within 4Å: Chain A: S.262, W.263, G.264, Y.267 Chain B: M.291, W.295 Ligands: 3PE.7, PC1.14 Ligand excluded by PLIP PC1.4: 12 residues within 4Å: Chain A: T.306, M.310 Chain D: I.224, M.227, L.228, M.278, L.279, L.318, I.319, L.322 Ligands: 3PE.8, PC1.38 Ligand excluded by PLIP PC1.5: 4 residues within 4Å: Chain A: H.201, D.234 Ligands: PC1.2, 3PE.8 Ligand excluded by PLIP PC1.9: 2 residues within 4Å: Chain A: V.221 Ligands: PC1.19 Ligand excluded by PLIP PC1.10: 8 residues within 4Å: Chain A: Q.245, M.291, S.292, W.295, L.299 Ligands: PC1.2, PC1.11, PC1.43 Ligand excluded by PLIP PC1.11: 7 residues within 4Å: Chain A: R.177, R.180, I.184, L.187, L.244 Ligands: PC1.2, PC1.10 Ligand excluded by PLIP PC1.14: 8 residues within 4Å: Chain B: Q.245, M.291, S.292, W.295, L.299 Ligands: PC1.3, PC1.15, PC1.17 Ligand excluded by PLIP PC1.15: 7 residues within 4Å: Chain B: R.177, R.180, I.184, L.187, L.244 Ligands: PC1.14, PC1.17 Ligand excluded by PLIP PC1.17: 11 residues within 4Å: Chain B: W.143, L.187, L.190, L.193, S.194, I.197, R.198, W.233 Ligands: PC1.14, PC1.15, PC1.20 Ligand excluded by PLIP PC1.18: 8 residues within 4Å: Chain B: S.262, W.263, G.264, Y.267 Chain C: M.291, W.295 Ligands: 3PE.22, PC1.26 Ligand excluded by PLIP PC1.19: 12 residues within 4Å: Chain A: I.224, M.227, L.228, M.278, L.279, L.318, I.319, L.322 Chain B: T.306, M.310 Ligands: PC1.9, 3PE.23 Ligand excluded by PLIP PC1.20: 4 residues within 4Å: Chain B: H.201, D.234 Ligands: PC1.17, 3PE.23 Ligand excluded by PLIP PC1.24: 2 residues within 4Å: Chain B: V.221 Ligands: PC1.31 Ligand excluded by PLIP PC1.26: 8 residues within 4Å: Chain C: Q.245, M.291, S.292, W.295, L.299 Ligands: PC1.18, PC1.27, PC1.29 Ligand excluded by PLIP PC1.27: 7 residues within 4Å: Chain C: R.177, R.180, I.184, L.187, L.244 Ligands: PC1.26, PC1.29 Ligand excluded by PLIP PC1.29: 11 residues within 4Å: Chain C: W.143, L.187, L.190, L.193, S.194, I.197, R.198, W.233 Ligands: PC1.26, PC1.27, PC1.32 Ligand excluded by PLIP PC1.30: 7 residues within 4Å: Chain C: S.262, W.263, G.264, Y.267 Chain D: W.295 Ligands: 3PE.34, PC1.39 Ligand excluded by PLIP PC1.31: 12 residues within 4Å: Chain B: I.224, M.227, L.228, M.278, L.279, L.318, I.319, L.322 Chain C: T.306, M.310 Ligands: PC1.24, 3PE.35 Ligand excluded by PLIP PC1.32: 4 residues within 4Å: Chain C: H.201, D.234 Ligands: PC1.29, 3PE.35 Ligand excluded by PLIP PC1.36: 2 residues within 4Å: Chain C: V.221 Ligands: PC1.44 Ligand excluded by PLIP PC1.38: 2 residues within 4Å: Chain D: V.221 Ligands: PC1.4 Ligand excluded by PLIP PC1.39: 8 residues within 4Å: Chain D: Q.245, M.291, S.292, W.295, L.299 Ligands: PC1.30, PC1.40, PC1.42 Ligand excluded by PLIP PC1.40: 7 residues within 4Å: Chain D: R.177, R.180, I.184, L.187, L.244 Ligands: PC1.39, PC1.42 Ligand excluded by PLIP PC1.42: 11 residues within 4Å: Chain D: W.143, L.187, L.190, L.193, S.194, I.197, R.198, W.233 Ligands: PC1.39, PC1.40, PC1.45 Ligand excluded by PLIP PC1.43: 7 residues within 4Å: Chain A: W.295 Chain D: S.262, W.263, G.264, Y.267 Ligands: PC1.10, 3PE.47 Ligand excluded by PLIP PC1.44: 12 residues within 4Å: Chain C: I.224, M.227, L.228, M.278, L.279, L.318, I.319, L.322 Chain D: T.306, M.310 Ligands: PC1.36, 3PE.48 Ligand excluded by PLIP PC1.45: 4 residues within 4Å: Chain D: H.201, D.234 Ligands: PC1.42, 3PE.48 Ligand excluded by PLIP

4 x PIE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL(Non-covalent)

PIE.6: 11 residues within 4Å: Chain A: N.29, F.31, S.61, D.62, F.65, Y.66, L.69, I.206, F.207, H.208, M.209 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.69, A:F.207 Hydrogen bonds: A:N.29, A:D.62, A:D.62, A:D.62, A:Y.66, A:H.208 PIE.21: 11 residues within 4Å: Chain B: N.29, F.31, S.61, D.62, F.65, Y.66, L.69, I.206, F.207, H.208, M.209 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.69, B:F.207 Hydrogen bonds: B:N.29, B:D.62, B:D.62, B:D.62, B:Y.66, B:H.208 PIE.33: 11 residues within 4Å: Chain C: N.29, F.31, S.61, D.62, F.65, Y.66, L.69, I.206, F.207, H.208, M.209 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.69, C:F.207 Hydrogen bonds: C:N.29, C:D.62, C:D.62, C:D.62, C:Y.66, C:H.208 PIE.46: 11 residues within 4Å: Chain D: N.29, F.31, S.61, D.62, F.65, Y.66, L.69, I.206, F.207, H.208, M.209 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.69, D:F.207 Hydrogen bonds: D:N.29, D:D.62, D:D.62, D:D.62, D:Y.66, D:H.208

8 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.7: 17 residues within 4Å: Chain A: L.73, V.76, G.77, I.81, V.84, G.85, F.89, D.91, E.92, T.94, W.97, F.100, H.232, Y.267, L.271 Ligands: PC1.3, 3PE.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.76, A:I.81, A:V.84, A:L.271 3PE.8: 22 residues within 4Å: Chain A: V.76, I.80, L.196, I.197, I.200, H.201, E.204, R.219, N.222, L.223, G.225, M.226, L.228, L.299, I.302, V.303, T.306, C.307, M.310 Ligands: PC1.4, PC1.5, 3PE.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.76, A:V.76, A:I.80, A:L.196, A:I.197, A:I.200, A:N.222, A:L.228, A:L.299, A:V.303, A:T.306 Hydrogen bonds: A:N.222 Salt bridges: A:H.201, A:H.201, A:R.219 3PE.22: 17 residues within 4Å: Chain B: L.73, V.76, G.77, I.81, V.84, G.85, F.89, D.91, E.92, T.94, W.97, F.100, H.232, Y.267, L.271 Ligands: PC1.18, 3PE.23 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.76, B:I.81, B:V.84, B:L.271 3PE.23: 22 residues within 4Å: Chain B: V.76, I.80, L.196, I.197, I.200, H.201, E.204, R.219, N.222, L.223, G.225, M.226, L.228, L.299, I.302, V.303, T.306, C.307, M.310 Ligands: PC1.19, PC1.20, 3PE.22 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.76, B:V.76, B:I.80, B:L.196, B:I.197, B:I.200, B:N.222, B:L.228, B:L.299, B:V.303, B:T.306 Hydrogen bonds: B:N.222 Salt bridges: B:H.201, B:H.201, B:R.219 3PE.34: 17 residues within 4Å: Chain C: L.73, V.76, G.77, I.81, V.84, G.85, F.89, D.91, E.92, T.94, W.97, F.100, H.232, Y.267, L.271 Ligands: PC1.30, 3PE.35 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.76, C:I.81, C:V.84, C:L.271 3PE.35: 22 residues within 4Å: Chain C: V.76, I.80, L.196, I.197, I.200, H.201, E.204, R.219, N.222, L.223, G.225, M.226, L.228, L.299, I.302, V.303, T.306, C.307, M.310 Ligands: PC1.31, PC1.32, 3PE.34 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:V.76, C:V.76, C:I.80, C:L.196, C:I.197, C:I.200, C:N.222, C:L.228, C:L.299, C:V.303, C:T.306 Hydrogen bonds: C:N.222 Salt bridges: C:H.201, C:H.201, C:R.219 3PE.47: 17 residues within 4Å: Chain D: L.73, V.76, G.77, I.81, V.84, G.85, F.89, D.91, E.92, T.94, W.97, F.100, H.232, Y.267, L.271 Ligands: PC1.43, 3PE.48 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.76, D:I.81, D:V.84, D:L.271 3PE.48: 22 residues within 4Å: Chain D: V.76, I.80, L.196, I.197, I.200, H.201, E.204, R.219, N.222, L.223, G.225, M.226, L.228, L.299, I.302, V.303, T.306, C.307, M.310 Ligands: PC1.44, PC1.45, 3PE.47 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:V.76, D:V.76, D:I.80, D:L.196, D:I.197, D:I.200, D:N.222, D:L.228, D:L.299, D:V.303, D:T.306 Hydrogen bonds: D:N.222 Salt bridges: D:H.201, D:H.201, D:R.219

4 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.12: 4 residues within 4Å: Chain A: H.208, D.212 Chain D: H.354, E.358 No protein-ligand interaction detected (PLIP) UNX.13: 4 residues within 4Å: Chain A: H.354, E.358 Chain B: H.208, D.212 No protein-ligand interaction detected (PLIP) UNX.25: 4 residues within 4Å: Chain B: H.354, E.358 Chain C: H.208, D.212 No protein-ligand interaction detected (PLIP) UNX.37: 4 residues within 4Å: Chain C: H.354, E.358 Chain D: H.208, D.212 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shintre, C.A. et al., Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel. To Be Published

Release Date

2019-05-01

Peptides

Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4: 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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Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4

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