Crystal Structure of membrane protein.

Basak, S; Schmandt, N; Chakrapani, S.

doi:10.2210/pdb5j0z/pdb

Macromolecule Content

Unique protein chains: 1

5J0Z

Crystal structure of GLIC in complex with DHA

DOI: 10.2210/pdb5j0z/pdb

Classification: MEMBRANE PROTEIN
Deposited: 2016-03-28 Released: 2017-03-15
Deposition author(s): Basak, S., Schmandt, N., Chakrapani, S.
Organism: Gloeobacter violaceus
Expression System: Escherichia coli

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.261
R-Value Work: 0.231

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: MEMBRANE PROTEIN

Total Structure Weight: 184340.00

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
Proton-gated ion channel	A, B, C, D, E	311	Gloeobacter violaceus	Gene Name(s): glvI glr4197
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: Q7NDN8 UniProt Full Protein Feature View for Q7NDN8 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for Q7NDN8/5J0Z

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Cys-Loop Receptor Family

Protein Name: Prokaryotic pentameric ligand-gated ion channel (GLIC)

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
PLC Query on PLC Download SDF File Download CCD File	A	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O	Poseview Image of PLC in 5J0Z 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)
LMT Query on LMT Download SDF File Download CCD File	A, B, D	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N	Poseview Image of LMT in 5J0Z 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)
HXA Query on HXA Download SDF File Download CCD File	A, B, C, D, E	DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID C₂₂ H₃₂ O₂ MBMBGCFOFBJSGT-KUBAVDMBSA-N	Poseview Image of HXA in 5J0Z 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 Query on SO4 Download SDF File Download CCD File	A, B, C, E	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L	Poseview Image of SO4 in 5J0Z 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)
ACT Query on ACT Download SDF File Download CCD File	A, E	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M	Poseview Image of ACT in 5J0Z 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, D, E	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M	Poseview Image of CL in 5J0Z 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)