› 2hpy

X-ray diffraction
2.8Å resolution

Crystallographic model of lumirhodopsin

Released:
DOI: 10.2210/pdb2hpy/pdb
PDB entry 2hpy coloured by chain, front view.
PDB entry 2hpy coloured by chain, side view.
PDB entry 2hpy coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Local peptide movement in the photoreaction intermediate of rhodopsin.
Nakamichi H, Okada T
Proc Natl Acad Sci U S A 103 12729-34 (2006)
PMID: 16908857

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136077 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Rhodopsin Chains: A, B
Molecule details ›
Chains: A, B
Length: 349 amino acids
Theoretical weight: 39.06 KDa
Source organism: Bos taurus
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, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
6 bound ligands:
Ligand HG 6 x HG
Ligand ZN 7 x ZN
Ligand RET 2 x RET
Ligand PLM 6 x PLM
Ligand HTG 4 x HTG
Ligand HTO 1 x HTO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P41
Unit cell:
a: 96.72Å b: 96.72Å c: 150.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.218 0.238

Quick links

Citations

35 review citations

A G protein-coupled receptor at work: the rhodopsin model.
Hofmann et al. (2009)
34 more

35 mentions without citation

Structure-function of the G protein-coupled receptor superfamily.
Katritch et al. (2013)
34 more