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Structure of bovine rhodopsin (dark adapted)

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

PDB: 1JFP
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: 5 · best druggability 0.85

Structure

solution nmr · 1 distinct chain · 27% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhodopsin	protein	309	27% helix, 1% 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

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	754	0.85	0.88	72	RET
2	194	0.57	0.80	28	empty
3	145	0.57	0.82	29	empty
4	192	0.55	0.79	31	empty
5	54	0.44	0.83	19	empty

Modifications

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

Compared structures

1JFP · Structure of bovine rhodopsin (dark adapted) · 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 0.65

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 1JFP · PDBe 1JFP · UniProt P02699

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