SMTL ID : 8ulg.1

Cryo-EM structure of bovine phosphodiesterase 6 bound to IBMX

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-mer

Ligands

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

PCG.1: 18 residues within 4Å: Chain A: R.93, M.94, S.95, 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, I.177, M.193 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.95, A:N.114, A:N.114, A:N.114, A:V.140, A:V.141, A:C.163, A:T.170, A:T.170, A:T.174, A:T.174 PCG.5: 19 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, D.165, 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:V.138, B:V.139, B:S.161, B:T.168, B:T.168, B:T.172, B:T.172

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: H.631 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: D.598, H.629 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.598

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.563, H.599, D.600, D.720 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.563, A:H.599, A:D.600 ZN.7: 4 residues within 4Å: Chain B: H.561, H.597, D.598, D.718 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.561, B:H.597, B:D.598, B:D.718

2 x IBM: 3-ISOBUTYL-1-METHYLXANTHINE(Non-covalent)

IBM.4: 3 residues within 4Å: Chain A: F.742, Q.773, F.776 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.773 pi-Stacking: A:F.776 IBM.8: 6 residues within 4Å: Chain B: Y.556, L.719, A.721, F.740, Q.771, F.774 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.740 Hydrogen bonds: B:Q.771 pi-Stacking: B:F.774

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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