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Structure of bovine rhodopsin (metarhodopsin II)

Analyse Structure of bovine rhodopsin (metarhodopsin II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LN6
Type: protein
Length: 309 residues
Chains: 1
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodopsin
UniProt: P02699
Ligands: RET
Pockets: 3 · best druggability 0.82

Structure

solution nmr · 1 distinct chain · 37% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhodopsin	protein	309	37% helix, 0% strand	P02699

Ligands and binding sites

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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	396	0.82	0.90	66	RET
2	103	0.50	0.81	21	empty
3	53	0.30	0.75	14	empty

Modifications

Observed in the structure: 5 cofactor, 1 disulfide (retinal Schiff base, disulfide).

Compared structures

1LN6 · STRUCTURE OF BOVINE RHODOPSIN (Metarhodopsin II) · the same entry in another collection · chain A against A, TM-score 1.00
P02699 · AlphaFold monomer V2.0 prediction for rhodopsin (P02699) · a predicted model of the same protein · chain A against A, TM-score 0.58

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 P02699
Elsewhere: RCSB PDB 1LN6 · PDBe 1LN6 · UniProt P02699

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