SMTL ID : 4kl1.1

HCN4 CNBD in complex with cGMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

8 x PCG: CYCLIC GUANOSINE MONOPHOSPHATE(Non-covalent)

PCG.1: 12 residues within 4Å: Chain A: V.128, F.144, G.145, E.146, I.147, C.148, R.155, T.156, A.157, V.159, R.196, L.197 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.145, A:E.146, A:E.146, A:I.147, A:C.148, A:T.156, A:T.156, A:T.156, A:R.196, A:R.199 Salt bridges: A:R.155 PCG.2: 10 residues within 4Å: Chain A: Y.45, K.48, M.49, F.50, E.52, E.53, F.99, R.166, Y.168 Chain C: H.27 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.45, A:K.48, A:F.50, A:Y.168, C:H.27 Salt bridges: A:R.166, C:H.27 pi-Stacking: A:F.50 PCG.6: 15 residues within 4Å: Chain B: I.109, V.128, L.138, F.144, G.145, E.146, I.147, C.148, R.155, T.156, A.157, V.159, R.196, L.197, R.199 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.145, B:E.146, B:E.146, B:I.147, B:C.148, B:T.156, B:T.156, B:T.156, B:R.196, B:R.196, B:R.199 Salt bridges: B:R.155 PCG.7: 10 residues within 4Å: Chain A: F.26, H.27 Chain B: Y.45, Q.46, K.48, M.49, F.50, E.52, F.99, R.166 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.48, B:K.48, B:F.50, A:H.27 Salt bridges: B:R.166, A:H.27 pi-Stacking: B:F.50 pi-Cation interactions: B:R.44 PCG.8: 14 residues within 4Å: Chain C: I.109, V.128, F.144, G.145, E.146, I.147, C.148, R.155, T.156, A.157, V.159, R.196, L.197, R.199 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.145, C:E.146, C:E.146, C:I.147, C:C.148, C:T.156, C:T.156, C:R.196, C:R.196, C:R.199 Salt bridges: C:R.155 PCG.9: 9 residues within 4Å: Chain C: Y.45, K.48, M.49, F.50, E.52, F.99, R.166 Chain D: F.26, H.27 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Y.45, C:K.48, C:F.50, C:Y.168, D:H.27 Salt bridges: C:R.166 pi-Stacking: C:F.50 pi-Cation interactions: C:R.44 Water bridges: D:H.27, D:H.27 PCG.13: 14 residues within 4Å: Chain D: I.109, V.128, T.130, F.144, G.145, E.146, I.147, C.148, R.155, T.156, A.157, V.159, R.196, R.199 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:T.130, D:G.145, D:E.146, D:E.146, D:I.147, D:C.148, D:T.156, D:T.156, D:R.196, D:R.196 Salt bridges: D:R.155 PCG.14: 11 residues within 4Å: Chain B: F.26, H.27 Chain D: R.44, Y.45, Q.46, K.48, F.50, E.52, F.99, R.166, Y.168 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.46, D:K.48, D:K.48, B:H.27 Salt bridges: D:R.166 pi-Stacking: D:F.50 pi-Cation interactions: D:R.44, D:R.44

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 6 residues within 4Å: Chain A: E.65, N.88, T.91, S.92, Y.182 Chain C: R.110 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain A Salt bridges: C:R.110 Hydrophobic interactions: A:N.88, A:T.91 Hydrogen bonds: A:E.65, A:Y.182 Water bridges: A:E.61 ACT.4: 4 residues within 4Å: Chain A: H.123, G.124, V.125, D.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.124 Salt bridges: A:H.123 ACT.5: 3 residues within 4Å: Chain A: K.137, L.138, A.139 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.139 ACT.12: 3 residues within 4Å: Chain C: D.39, E.42, H.43 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:D.39 Hydrogen bonds: C:D.39, C:E.42 Salt bridges: C:H.43

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: N.88 Chain C: Y.107, R.110, K.131, S.158 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:N.88, A:N.88, C:K.131, C:S.158, C:S.158 GOL.11: 6 residues within 4Å: Chain C: E.61, P.62, E.65 Chain D: Y.107, I.108, R.110 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.110, C:E.61 Water bridges: D:Y.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lolicato, M. et al., Cyclic dinucleotides bind the C-linker of HCN4 to control channel cAMP responsiveness. Nat.Chem.Biol. (2014)

Release Date

2014-04-30

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

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