3CAP

Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.229

Literature

Macromolecules
Sequence Display for 3CAP

Classification: SIGNALING PROTEIN

Total Structure Weight: 82676.88

Macromolecule Entities
Molecule Chains Length Organism Details
Rhodopsin A, B 348 Bos taurus Details: this protein is Ligand-free rhodopsin, Opsin.
Gene Name(s): RHO Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: Rhodopsin


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BGL
Query on BGL

A, B B-2-OCTYLGLUCOSIDE
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLM
Query on PLM

A, B PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A, B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.229
  • Space Group: H 3

Unit Cell:

Length (Å) Angle (°)
a = 242.92 α = 90.00
b = 242.92 β = 90.00
c = 110.42 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-02-20
  • Released Date: 2008-06-24
  • Deposition author(s): Park, J.H., Scheerer, P., Hofmann, K.P., Choe, H.-W., Ernst, O.P.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update