Biological Assembly 1

Protein Symmetry: Cyclic - C2 (View in 3D)

Protein Stoichiometry: Homo 2-mer - A2

Macromolecule Content

• Unique protein chains: 1

1VGO

Crystal Structure of Archaerhodopsin-2

• DOI: 10.2210/pdb1vgo/pdb

• Classification: PROTON TRANSPORT
• Deposited: 2004-04-28 Released: 2005-10-04
• Deposition author(s): Yoshimura, K., Enami, N., Murakami, M., Okumura, H., Ihara, K., Kouyama, T.
• Organism: Halobacterium sp. AUS-2

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.268
• R-Value Work: 0.241

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: PROTON TRANSPORT

Total Structure Weight: 59159.73

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Bacterial and Algal Rhodopsins

Protein Name: Archaerhodopsin-2 (aR-2)

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
BNG	A, B	B-NONYLGLUCOSIDE C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N	Poseview Image of BNG in 1VGO Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)
RET	A, B	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N	Poseview Image of RET in 1VGO Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L	Poseview Image of SO4 in 1VGO Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL   Binding Pocket (JSmol)   Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.268
• R-Value Work: 0.241
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 122.88	α = 90.00
b = 139.48	β = 90.00
c = 108.10	γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

• Deposited Date: 2004-04-28
• Released Date: 2005-10-04
• Deposition author(s): Yoshimura, K., Enami, N., Murakami, M., Okumura, H., Ihara, K., Kouyama, T.

Revision History

• 2008-04-27
  Type: Version format compliance
• 2011-07-13
  Type: Version format compliance