SMTL ID : 8ugs.1

Cryo-EM structure of bovine phosphodiesterase 6 bound to cGMP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-mer

Ligands

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

PCG.1: 18 residues within 4Å: Chain A: M.94, S.95, F.97, F.113, N.114, F.134, G.139, V.140, V.141, F.162, C.163, V.166, D.167, T.170, Y.172, T.174, M.193, V.195 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.114, A:N.114, A:V.140, A:V.141, A:H.161, A:C.163, A:T.170, A:T.170, A:T.174, A:T.174 pi-Stacking: A:F.113 PCG.4: 12 residues within 4Å: Chain A: H.559, H.563, D.600, L.671, D.720, L.721, V.738, F.742, Q.773, F.776 Ligands: ZN.2, MG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.773, A:Q.773 Salt bridges: A:H.559 pi-Stacking: A:F.776 pi-Cation interactions: A:F.776 PCG.5: 18 residues within 4Å: Chain B: R.91, C.92, S.93, F.111, S.112, F.132, G.137, V.138, V.139, F.160, S.161, A.164, T.168, Y.170, T.172, I.175, M.191, V.193 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.93, B:S.112, B:S.112, B:S.112, B:S.112, B:V.138, B:V.139, B:S.161, B:T.172, B:T.172 PCG.8: 12 residues within 4Å: Chain B: H.557, H.561, D.598, L.669, D.718, L.719, V.736, F.740, M.758, Q.771, F.774 Ligands: MG.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.771, B:Q.771 Salt bridges: B:H.557, B:H.561, B:H.597 pi-Stacking: B:F.774 pi-Cation interactions: B:F.774

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.563, H.599, D.600, D.720 Ligands: PCG.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.563, A:H.599, A:D.600, A:D.720, A:D.720 ZN.6: 4 residues within 4Å: Chain B: H.561, H.597, D.598, D.718 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.561, B:H.597, B:H.597, B:D.598, B:D.598

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.600, E.628 Ligands: PCG.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.600 MG.7: 3 residues within 4Å: Chain B: H.597, D.598 Ligands: PCG.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.598

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aplin, C. et al., Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6. J.Biol.Chem. (2023)

Release Date

2024-01-17

Peptides

Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha: A
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta: B
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta

Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma

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