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Crystal structure of bovine rhodopsin

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

PDB: 1F88
Type: protein
Length: 643 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodopsin
UniProt: P02699
Ligands: RET, NAG, MAN, HG, ZN
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhodopsin	protein	338	63% helix, 4% strand	P02699
B	Rhodopsin	protein	305	66% helix, 4% strand	P02699

Ligands and binding sites

RET · Retinal · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar
HG · Mercury (II) ion · metal · 6 copies · chains A, B
ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

7 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	146	0.82	0.98	33	RET
2	141	0.81	0.97	29	RET
3	704	0.68	0.76	60	HG
4	441	0.62	0.76	54	empty
5	186	0.50	0.77	25	empty

Interfaces

1 interface between chains.

A–B · 838 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 2 cofactor, 2 disulfide (N-glycosylation, retinal Schiff base, disulfide).

Compared structures

1F88 · Crystal structure of bovine rhodopsin · 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 B against A, TM-score 0.92

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 1F88 · PDBe 1F88 · UniProt P02699

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