SMTL ID : 9cxg.1

Structure of PDE6C in complex with inhibitory cone p gamma in the presence of cGMP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

PCG.1: 17 residues within 4Å: Chain A: R.108, C.109, S.110, L.128, D.129, F.149, G.154, I.155, V.156, F.177, S.178, M.181, D.182, T.185, T.189, L.192, V.210 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.110, A:D.129, A:D.129, A:I.155, A:V.156, A:S.178, A:T.185, A:T.185, A:T.189 Salt bridges: A:D.129 PCG.5: 16 residues within 4Å: Chain B: R.108, C.109, S.110, L.128, D.129, G.154, I.155, V.156, H.176, F.177, S.178, M.181, D.182, T.185, T.189, L.192 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.129, B:I.155, B:V.156, B:H.176, B:S.178, B:T.189 Salt bridges: B:D.129

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.579, H.615, D.616, D.736 Ligands: 5GP.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.579, A:H.615, A:D.616, A:D.736 ZN.6: 5 residues within 4Å: Chain B: H.579, H.615, D.616, D.736 Ligands: 5GP.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.579, B:H.615, B:D.616, B:D.736, 5GP.8

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: H.615, D.616, E.644, H.647 Ligands: 5GP.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.616, 5GP.4 MG.7: 4 residues within 4Å: Chain B: D.616, H.647, T.685 Ligands: 5GP.8 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: 5GP.8, 5GP.8

2 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.4: 15 residues within 4Å: Chain A: H.575, H.579, H.615, D.616, H.619, T.685, L.687, D.736, L.737, I.740, F.758, Q.789, F.792 Ligands: ZN.2, MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.575, A:Q.789, A:Q.789 Salt bridges: A:H.575 pi-Stacking: A:F.792 pi-Cation interactions: A:F.792 5GP.8: 15 residues within 4Å: Chain B: Y.574, H.575, H.579, H.615, D.616, H.619, T.685, L.687, D.736, L.737, F.758, Q.789, F.792 Ligands: ZN.6, MG.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.575, B:Q.789, B:Q.789 Salt bridges: B:H.575, B:H.579 pi-Stacking: B:F.792 pi-Cation interactions: B:F.792

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S. et al., Structural and functional dynamics of human cone cGMP-phosphodiesterase important for photopic vision. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2024-12-18

Peptides

Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha': AB
cone P gamma: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'

cone P gamma

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