SMTL ID : 9cxi.1

Structure of PDE6C in complex with the rod inhibitory p gamma subunit in the absence of added cGMP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.616, T.685, D.736 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.616, A:D.616 MG.5: 2 residues within 4Å: Chain B: D.616, E.644 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.616

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

PCG.3: 15 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.110, A:D.129, A:I.155, A:V.156, A:S.178, A:T.185 Salt bridges: A:D.129 PCG.6: 15 residues within 4Å: Chain B: R.108, S.110, L.128, D.129, G.154, I.155, V.156, F.177, S.178, M.181, T.185, Y.187, T.189, L.192, M.208 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.110, B:D.129, B:I.155, B:V.156, B:S.178 Salt bridges: B:D.129

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
rod pg: 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'

rod pg

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