1L9H

Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 1L9H

Classification: SIGNALING PROTEIN

Total Structure Weight: 86675.08

Macromolecule Entities
Molecule Chains Length Organism Details
rhodopsin A, B 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 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BNG
Query on BNG

A, B B-NONYLGLUCOSIDE
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RET
Query on RET

A, B RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-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)
HG
Query on HG

A, B MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

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

A HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-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 NON-POLYMER C2 H4 O --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.188
  • Space Group: P 41

Unit Cell:

Length (Å) Angle (°)
a = 96.75 α = 90.00
b = 96.75 β = 90.00
c = 149.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-03-23
  • Released Date: 2002-05-15
  • Deposition author(s): Okada, T., Fujiyoshi, Y., Silow, M., Navarro, J., Landau, E.M., Shichida, Y.

Revision History

  • 2008-04-28
    Type: Version format compliance
  • 2011-07-13
    Type: Derived calculations, Version format compliance