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Crystal structure of squid rhodopsin

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

PDB: 2ZIY
Type: protein
Length: 370 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodopsin
UniProt: P31356
Ligands: PLM, RET
Pockets: 3 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 68% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhodopsin	protein	370	68% helix, 2% strand	P31356

Ligands and binding sites

PLM · Palmitic acid · ligand · 2 copies · chains A
RET · Retinal · ligand · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	237	0.83	0.95	28	RET
2	706	0.74	0.79	81	empty
3	69	0.40	0.79	14	empty

Modifications

Observed in the structure: 2 lipid, 1 cofactor, 1 disulfide (palmitoylation, retinal Schiff base, disulfide).

Compared structures

2ZIY · Crystal structure of squid rhodopsin · the same entry in another collection · chain A against A, TM-score 1.00
P31356 · AlphaFold monomer V2.0 prediction for rhodopsin (P31356) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P31356
Elsewhere: RCSB PDB 2ZIY · PDBe 2ZIY · UniProt P31356

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