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The crystal structure of PDE6D in complex with rac-S1

Analyse The crystal structure of PDE6D in complex with rac-S1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JV8
Type: protein
Length: 147 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta
UniProt: O43924
Ligands: 1M1
Pockets: 1 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta	protein	147	14% helix, 59% strand	O43924

Ligands and binding sites

1M1 · (6R)-6-(pyridin-2-yl)-5,6-dihydrobenzimidazo[1,2-c]quinazoline · ligand · 2 copies · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	392	0.82	0.90	40	1M1

Compared structures

4JV8 · The crystal structure of PDE6D in complex with rac-S1 · the same entry in another collection · chain B against B, TM-score 1.00
O43924 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 O43924
Elsewhere: RCSB PDB 4JV8 · PDBe 4JV8 · UniProt O43924

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