Research workbench

Crystal structure of PDE6D Geranylgeranylated cystein complex

Analyse Crystal structure of PDE6D Geranylgeranylated cystein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7Q9Q
Type: protein
Length: 148 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.45
Source: Homo sapiens
Molecule: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
UniProt: O43924
Ligands: CMT, GER
Pockets: 1 · best druggability 0.82

Structure

x-ray diffraction · resolution 1.45 · 1 distinct chain · 14% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
BBB	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	protein	148	14% helix, 59% strand	O43924

Ligands and binding sites

CMT · O-methylcysteine · ligand · chains BBB
GER · Geran-8-yl geran · ligand · chains BBB
EDO · 1,2-ethanediol · additive · 3 copies · chains BBB

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	421	0.82	0.89	43	CMT, GER

Compared structures

O43924 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain BBB against A, TM-score 0.97

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 7Q9Q · PDBe 7Q9Q · UniProt O43924

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.