› 6fkd

X-ray diffraction
2.49Å resolution

Crystal structure of N2C/D282C stabilized opsin bound to RS16

Released:
DOI: 10.2210/pdb6fkd/pdb
PDB entry 6fkd coloured by chain, front view.
PDB entry 6fkd coloured by chain, side view.
PDB entry 6fkd coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Ligand channel in pharmacologically stabilized rhodopsin.
Mattle D, Kuhn B, Aebi J, Bedoucha M, Kekilli D, Grozinger N, Alker A, Rudolph MG, Schmid G, Schertler GFX, Hennig M, Standfuss J, Dawson RJP
Proc Natl Acad Sci U S A 115 3640-3645 (2018)
PMID: 29555765

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136065 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Rhodopsin Chain: A
Molecule details ›
Chain: A
Length: 349 amino acids
Theoretical weight: 39.03 KDa
Source organism: Bos taurus
Expression system: Homo sapiens
UniProt:
  • Canonical: P02699 (Residues: 1-348; Coverage: 100%)
Gene name: RHO
Sequence domains:
Structure domains: Rhodopsin 7-helix transmembrane proteins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand PLM 1 x PLM
Ligand BOG 5 x BOG
Ligand DL2 1 x DL2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: R32
Unit cell:
a: 243.431Å b: 243.431Å c: 111.782Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.229 0.228 0.25
Expression system: Homo sapiens

Quick links

Citations

6 review citations

The Retinoid and Non-Retinoid Ligands of the Rod Visual G Protein-Coupled Receptor.
Ortega et al. (2019)
5 more

2 mentions without citation

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.
Enkavi et al. (2019)
1 more