4J4Q

Crystal structure of active conformation of GPCR opsin stabilized by octylglucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.217

Literature

Macromolecules
Sequence Display for 4J4Q

Classification: SIGNALING PROTEIN

Total Structure Weight: 43115.04

Macromolecule Entities
Molecule Chains Length Organism Details
Rhodopsin A 348 Bos taurus Gene Name(s): RHO Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Guanine nucleotide-binding protein G(t) subunit alpha-1 B 11 Bos taurus Fragment: C-terminal derived peptide, UNP RESIDUES 340-350
Mutation: K341L, C347V
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 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TRE
Query on TRE

A TREHALOSE
ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GLUCOPYRANOSIDE (Synonym)
C12 H22 O11
HDTRYLNUVZCQOY-LIZSDCNHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.217
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 241.26 α = 90.00
b = 241.26 β = 90.00
c = 109.56 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-02-07
  • Released Date: 2013-10-30
  • Deposition author(s): Park, J.H., Morizumi, T., Li, Y., Hong, J.E., Pai, E.F., Hofmann, K.P., Choe, H.W., Ernst, O.P.

Revision History

No revisions since initial release