Crystal Structures of Human GlyR alpha 3 Bound to Ivermectin.

Huang, X; Chen, H; Shaffer, P.L.

Macromolecule Content

Unique protein chains: 1

5VDH

Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607, Glycine, and Ivermectin

DOI: 10.2210/pdb5vdh/pdb

Classification: TRANSPORT PROTEIN
Deposited: 2017-04-03 Released: 2017-05-24
Deposition author(s): Shaffer, P.L., Huang, X., Chen, H.
Organism: Homo sapiens
Expression System: Spodoptera frugiperda

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.236
R-Value Work: 0.226

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: TRANSPORT PROTEIN

Total Structure Weight: 216628.70

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
Glycine receptor subunit alpha-3	A, B, C, D, E	362	Homo sapiens	Fragment: UNP residues 34-342, ATG linker, UNP residues 419-460 Gene Name(s): GLRA3 Gene View
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: O75311 UniProt Full Protein Feature View for O75311 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for O75311/5VDH

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Cys-Loop Receptor Family

Protein Name: α1 GlyR Glycine receptor in complex with strychnine

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
IVM Query on IVM Download SDF File Download CCD File	A, B, C, D, E	(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)- 6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19- tetramethyl-17-oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b- tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2- pq][2,6]benzodioxacyclooctadecine-13,2'-pyran]- 7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl- alpha-L-arabino-hexopyranosyl)-3-O-methyl- alpha-L-arabino-hexopyranoside 22,23-DIHYDROAVERMECTIN B1A; IVERMECTIN (Synonym) C₄₈ H₇₄ O₁₄ AZSNMRSAGSSBNP-XPNPUAGNSA-N	Poseview Image of IVM in 5VDH 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)
7C6 Query on 7C6 Download SDF File Download CCD File	A, B, C, D, E	(3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]- 3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4- c][1,6]naphthyridin-4-one C₁₉ H₁₉ N₃ O₅ S MXNQASHPCAMJHG-UCMVZMLTSA-N	Poseview Image of 7C6 in 5VDH 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)
NAG Query on NAG Download SDF File Download CCD File	C	N-ACETYL-D-GLUCOSAMINE C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N	Poseview Image of NAG in 5VDH 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)
GLY Query on GLY Download SDF File Download CCD File	A, B, C, D, E	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N	Poseview Image of GLY in 5VDH 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)
ZN Query on ZN Download SDF File Download CCD File	A, B, C, D, E	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N	Poseview Image of ZN in 5VDH 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	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M	Poseview Image of CL in 5VDH 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)