2I37

Crystal structure of a photoactivated rhodopsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.15 Å
  • R-Value Free: 0.382
  • R-Value Work: 0.377

Literature

Macromolecules
Sequence Display for 2I37

Classification: MEMBRANE PROTEIN

Total Structure Weight: 120948.96

Macromolecule Entities
Molecule Chains Length Organism Details
Rhodopsin A, B, C 349 Bos taurus 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
NDG
Query on NDG

B, C 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
A, B, C NON-POLYMER C2 H4 O --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.15 Å
  • R-Value Free: 0.382
  • R-Value Work: 0.377
  • Space Group: P 31 1 2

Unit Cell:

Length (Å) Angle (°)
a = 161.24 α = 90.00
b = 161.24 β = 90.00
c = 143.44 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-08-17
  • Released Date: 2006-10-17
  • Deposition author(s): Lodowski, D.T., Stenkamp, R.E., Salom, D., Le Trong, I., Palczewski, K.

Revision History

  • Version 1_0: 2006-10-17

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Non-polymer description, Version format compliance

  • Version 1_3: 2017-10-18

    Type: Refinement description