SMTL ID : 6mzb.1

Cryo-EM structure of phosphodiesterase 6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.557, H.561, V.565, H.597, D.598, D.718 Ligands: MG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.561, A:H.597, A:D.598 ZN.4: 7 residues within 4Å: Chain B: H.559, H.563, V.567, H.599, D.600, D.720 Ligands: MG.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.563, B:H.599, B:D.600, B:D.720

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.626, H.629, T.667 Ligands: ZN.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: D.600, T.669 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.600, B:D.600

2 x 35G: GUANOSINE-3',5'-MONOPHOSPHATE(Non-covalent)

35G.3: 20 residues within 4Å: Chain A: R.91, C.92, S.93, F.95, F.111, S.112, F.132, I.136, G.137, V.138, V.139, F.160, S.161, A.164, T.168, Y.170, T.172, I.175, M.191, V.193 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.93, A:S.93, A:V.138, A:V.139, A:S.161, A:S.161 pi-Cation interactions: A:F.111 35G.6: 21 residues within 4Å: Chain B: R.93, M.94, S.95, F.97, F.113, N.114, V.115, F.134, V.140, V.141, F.162, C.163, D.164, V.166, D.167, T.170, Y.172, T.174, I.177, M.193, V.195 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.95, B:N.114, B:N.114, B:N.114, B:V.140, B:C.163, B:T.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gulati, S. et al., Cryo-EM structure of phosphodiesterase 6 reveals insights into the allosteric regulation of type I phosphodiesterases. Sci Adv (2019)

Release Date

2019-03-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

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

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

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

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