3DQB

Crystal structure of the active G-protein-coupled receptor opsin in complex with a C-terminal peptide derived from the Galpha subunit of transducin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 3DQB

Classification: SIGNALING PROTEIN

Total Structure Weight: 42932.05

Macromolecule Entities
Molecule Chains Length Organism Details
Rhodopsin A 348 Bos taurus Details: this protein is Ligand-free rhodopsin, Opsin.
Gene Name(s): RHO Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
11meric peptide form Guanine nucleotide-binding protein G(t) subunit alpha-1 B 11 Bos taurus Fragment: C-terminal domain, UNP residues 340-350
Mutation: K341L
Gene Name(s): GNAT1 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 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BOG
Query on BOG

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

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

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

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A 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: 3.2 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.213
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 238.02 α = 90.00
b = 238.02 β = 90.00
c = 109.13 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-09
  • Released Date: 2008-09-23
  • Deposition author(s): Scheerer, P., Park, J.H., Hildebrand, P.W., Kim, Y.J., Krauss, N., Choe, H.-W., Hofmann, K.P., Ernst, O.P.

Revision History

  • 2011-07-13
    Type: Non-polymer description, Version format compliance
  • 2014-02-05
    Type: Derived calculations