Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis.

Kouyama, T; Kanada, S; Takeguchi, Y; Narusawa, A; Murakami, M; Ihara, K.

Macromolecule Content

Unique protein chains: 1

3A7K

Crystal structure of halorhodopsin from Natronomonas pharaonis

DOI: 10.2210/pdb3a7k/pdb

Classification: MEMBRANE PROTEIN
Deposited: 2009-09-27 Released: 2009-12-15
Deposition author(s): Kouyama, T.
Organism: Natronomonas pharaonis

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.0 Å
R-Value Free: 0.274
R-Value Work: 0.249

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: MEMBRANE PROTEIN

Total Structure Weight: 110300.57

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
Halorhodopsin	A, B, D	291	Natronomonas pharaonis	Gene Name(s): hop NP_0642A
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: Q3ITX1 UniProt Full Protein Feature View for Q3ITX1 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for Q3ITX1/3A7K

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Bacterial and Algal Rhodopsins

Protein Name: Halorhodopsin (HR)

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
L3P Query on L3P Download SDF File Download CCD File	A, B, D	2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL- 3'-SN-GLYCEROL-1'-PHOSPHATE C₄₆ H₉₄ O₁₁ P₂ TZXJQSKPTCRGCA-VZSPAKCESA-L	Poseview Image of L3P in 3A7K 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)
22B Query on 22B Download SDF File Download CCD File	A, B, D	BACTERIORUBERIN C₅₀ H₇₆ O₄ UVCQMCCIAHQDAF-CUMPQFAQSA-N	Poseview Image of 22B in 3A7K 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)
L1P Query on L1P Download SDF File Download CCD File	A, B	3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)- SN-GLYCERO-3-PHOSPHATE (Synonym) C₄₃ H₈₉ O₆ P UKQGAMWGTOTQPC-ALOLAALWSA-N	Poseview Image of L1P in 3A7K 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)
L2P Query on L2P Download SDF File Download CCD File	A, B, D	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 3A7K 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 Query on RET Download SDF File Download CCD File	A, B, D	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N	Poseview Image of RET in 3A7K 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)
CL Query on CL Download SDF File Download CCD File	A, B, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M	Poseview Image of CL in 3A7K 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)