Biological Assembly 1

Protein Symmetry: Cyclic - C3 (View in 3D)

Protein Stoichiometry: Homo 3-mer - A3

Macromolecule Content

• Unique protein chains: 1

5B6Z

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 1.725 ms us after photoexcitation

• DOI: 10.2210/pdb5b6z/pdb

• Classification: PROTON TRANSPORT
• Deposited: 2016-06-02 Released: 2016-12-21
• Deposition author(s): Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.
• Organism: Halobacterium salinarum

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.186
• R-Value Work: 0.168

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: PROTON TRANSPORT

Total Structure Weight: 30891.94

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Bacterial and Algal Rhodopsins

Protein Name: Bacteriorhodopsin (BR)

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
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	Poseview Image of L2P in 5B6Z 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	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N	Poseview Image of RET in 5B6Z 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)
MYS	A	PENTADECANE C15 H32 YCOZIPAWZNQLMR-UHFFFAOYSA-N	Poseview Image of MYS in 5B6Z 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)
C14	A	TETRADECANE C14 H30 BGHCVCJVXZWKCC-UHFFFAOYSA-N	Poseview Image of C14 in 5B6Z 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)
TRD	A	TRIDECANE LIPID FRAGMENT (Synonym) C13 H28 IIYFAKIEWZDVMP-UHFFFAOYSA-N	Poseview Image of TRD in 5B6Z 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)
UND	A	UNDECANE LIPID FRAGMENT (Synonym) C11 H24 RSJKGSCJYJTIGS-UHFFFAOYSA-N	Poseview Image of UND in 5B6Z 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)
D10	A	DECANE C10 H22 DIOQZVSQGTUSAI-UHFFFAOYSA-N	Poseview Image of D10 in 5B6Z 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)
DD9	A	nonane C9 H20 BKIMMITUMNQMOS-UHFFFAOYSA-N	Poseview Image of DD9 in 5B6Z 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)
OCT	A	N-OCTANE C8 H18 TVMXDCGIABBOFY-UHFFFAOYSA-N	Poseview Image of OCT in 5B6Z 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)
HP6	A	HEPTANE C7 H16 IMNFDUFMRHMDMM-UHFFFAOYSA-N	Poseview Image of HP6 in 5B6Z 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: 2.1 Å
• R-Value Free: 0.186
• R-Value Work: 0.168
• Space Group: P 6₃

Unit Cell:

Length (Å)	Angle (°)
a = 62.50	α = 90.00
b = 62.50	β = 90.00
c = 112.00	γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

• Deposited Date: 2016-06-02
• Released Date: 2016-12-21
• Deposition author(s): Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

Revision History

• 2017-02-01
  Type: Database references