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Structure of the visual signaling complex between transducin and phosphodiesterase 6

Analyse Structure of the visual signaling complex between transducin and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JSN
Type: protein
Length: 2,400 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rod cgmp-specific 3',5'-cyclic phosphodiesterase subunit alpha; Rod cgmp-specific…
EC: 3.1.4.35
UniProt: P11541, P23439, P04695, P04972
Ligands: VDN, 35G, GTP, ZN, MG
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 4 distinct chains · 46% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rod cgmp-specific 3',5'-cyclic phosphodiesterase subunit alpha (EC 3.1.4.35)	protein	820	48% helix, 10% strand	P11541
B	Rod cgmp-specific 3',5'-cyclic phosphodiesterase subunit beta (EC 3.1.4.35)	protein	806	47% helix, 10% strand	P23439
E, F	Guanine nucleotide-binding protein G(T) subunit alpha-1, guanine nucleotide-binding protein G(I) subunit alpha-1 chimera	protein	316	45% helix, 14% strand	P04695
C, D	Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit gamma (EC 3.1.4.35)	protein	71	13% helix, 3% strand	P04972

Ligands and binding sites

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 · ligand · 2 copies · chains A, B
35G · Guanosine-3',5'-monophosphate · ligand · 2 copies · chains A, B
GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains E, F
ZN · Zinc ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1054	0.81	0.82	93	empty
2	692	0.80	0.84	65	GTP
3	185	0.79	0.94	27	35G
4	712	0.78	0.82	76	empty
5	276	0.77	0.89	35	35G

Interfaces

11 interfaces between chains.

A–B · 5988 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1616 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 1543 Å² buried · 7 hydrogen bonds · protein-protein
F–D · 1270 Å² buried · 7 hydrogen bonds · protein-protein
E–C · 1186 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7JSN · Structure of the Visual Signaling Complex between Transducin and Phosphodiesterase 6 · the same entry in another collection · chain D against D, TM-score 1.00
P04695 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(T) subunit… · a predicted model of the same protein · chain E against A, TM-score 0.96
P23439 · AlphaFold monomer V2.0 prediction for rod cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain B against A, TM-score 0.93
P11541 · AlphaFold monomer V2.0 prediction for rod cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain A against A, TM-score 0.92
P04972 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain C against A, TM-score 0.26

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P11541
Every structure of UniProt P23439
Every structure of UniProt P04695
Every structure of UniProt P04972
Elsewhere: RCSB PDB 7JSN · PDBe 7JSN · UniProt P11541 · UniProt P23439 · UniProt P04695 · UniProt P04972

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