3QAP

Crystal structure of Natronomonas pharaonis sensory rhodopsin II in the ground state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.152

Literature

Macromolecules
Sequence Display for 3QAP

Classification: TRANSPORT PROTEIN

Total Structure Weight: 35445.80

Macromolecule Entities
Molecule Chains Length Organism Details
Sensory rhodopsin-2 A 239 Natronomonas pharaonis Gene Name(s): sop2 sopII
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Bacterial and Algal Rhodopsins

Protein Name: Sensory Rhodopsin II (SRII)


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
L2P
Query on L2P

A 2,3-DI-PHYTANYL-GLYCEROL
1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)- SN-GLYCEROL (Synonym)
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-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)
RET
Query on RET

A RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LFA
Query on LFA

A EICOSANE
LIPID FRAGMENT (Synonym)
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.152
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 86.99 α = 90.00
b = 128.09 β = 90.00
c = 50.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-11
  • Released Date: 2011-09-14
  • Deposition author(s): Gushchin, I., Reshetnyak, A., Borshchevskiy, V., Ishchenko, A., Round, E., Grudinin, S., Engelhard, M., Buldt, G., Gordeliy, V.

Revision History

  • 2011-09-28
    Type: Database references