SMTL ID : 7jsn.1

Structure of the Visual Signaling Complex between Transducin and Phosphodiesterase 6

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.563, H.599, D.600, D.720 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.563, A:H.599, A:D.600, A:D.720 ZN.5: 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 MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.600 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.600 MG.6: 1 residues within 4Å: Chain B: D.598 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.598

2 x VDN: 2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE(Non-covalent)

VDN.3: 7 residues within 4Å: Chain A: Y.558, A.739, F.742, M.760, L.769, Q.773, F.776 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.739, A:F.742, A:L.769, A:F.776 Hydrogen bonds: A:Q.773 pi-Stacking: A:F.776 VDN.7: 6 residues within 4Å: Chain B: Y.556, A.733, M.758, L.767, Q.771, F.774 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.767, B:F.774 Hydrogen bonds: B:Q.771 pi-Stacking: B:F.774

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

35G.4: 19 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, V.195 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.95, A:N.114, A:V.140, A:V.141, A:C.163, A:T.170, A:T.170 pi-Stacking: A:F.113 35G.8: 18 residues within 4Å: Chain B: R.91, C.92, S.93, F.111, S.112, F.132, G.137, V.138, V.139, S.161, A.164, D.165, T.168, Y.170, T.172, I.175, M.191, V.193 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.93, B:S.112, B:V.138, B:V.139, B:S.161, B:T.168, B:T.172 pi-Stacking: B:F.111

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.9: 22 residues within 4Å: Chain C: G.47, E.48, S.49, G.50, K.51, S.52, T.53, D.155, S.156, R.181, S.182, C.183, V.184, K.185, T.186, G.208, K.275, D.277, L.278, C.330, A.331, T.332 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:E.48, C:E.48, C:S.49, C:G.50, C:K.51, C:S.52, C:T.53, C:D.155, C:S.156, C:V.184, C:T.186, C:T.186, C:V.206, C:G.208, C:K.275, C:A.331, C:T.332, C:T.332 Salt bridges: C:K.51, C:K.51, C:D.155, C:D.277 GTP.10: 20 residues within 4Å: Chain D: E.48, S.49, G.50, K.51, S.52, T.53, D.155, S.156, R.181, S.182, C.183, V.184, K.185, T.186, G.208, K.275, D.277, L.278, C.330, A.331 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:E.48, D:S.49, D:G.50, D:K.51, D:S.52, D:T.53, D:S.156, D:S.156, D:S.156, D:R.181, D:S.182, D:V.184, D:V.184, D:T.186, D:T.186, D:G.208, D:K.275, D:A.331 Salt bridges: D:K.51, D:K.51, D:D.155, D:K.185, D:D.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Y. et al., Structure of the Visual Signaling Complex between Transducin and Phosphodiesterase 6. Mol.Cell (2020)

Release Date

2020-10-21

Peptides

Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha: A
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta: B
Guanine nucleotide-binding protein G(t) subunit alpha-1, Guanine nucleotide-binding protein G(i) subunit alpha-1 chimera: CD
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

E
C

F
D

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

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

Guanine nucleotide-binding protein G(t) subunit alpha-1, Guanine nucleotide-binding protein G(i) subunit alpha-1 chimera

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

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