Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 96110.52 
• Atom Count: 5071 
• Residue Count: 848 
• Unique protein chains: 1

5DHG

The crystal structure of nociceptin/orphanin FQ peptide receptor (NOP) in complex with C-35 (PSI Community Target)

• DOI: 10.2210/pdb5DHG/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): 3 


• Deposited: 2015-08-30 Released: 2015-10-21 
• Deposition Author(s): Miller, R.L., Thompson, A.A., Trapella, C., Guerrini, R., Malfacini, D., Patel, N., Han, G.W., Cherezov, V., Calo, G., Katritch, V., Stevens, R.C., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.275 
• R-Value Work: 0.235 

Literature

The Importance of Ligand-Receptor Conformational Pairs in Stabilization: Spotlight on the N/OFQ G Protein-Coupled Receptor.

Miller, R.L., Thompson, A.A., Trapella, C., Guerrini, R., Malfacini, D., Patel, N., Han, G.W., Cherezov, V., Calo, G., Katritch, V., Stevens, R.C.

(2015) Structure 23: 2291-2299

• PubMed: 26526853 
• DOI: 10.1016/j.str.2015.07.024
• Primary Citation of Related Structures:  
  5DHH


• PubMed Abstract: 
  

Understanding the mechanism by which ligands affect receptor conformational equilibria is key in accelerating membrane protein structural biology. In the case of G protein-coupled receptors (GPCRs), we currently pursue a brute-force approach for identifying ligands that stabilize receptors and facilitate crystallogenesis. The nociceptin/orphanin FQ peptide receptor (NOP) is a member of the opioid receptor subfamily of GPCRs for which many structurally diverse ligands are available for screening. We observed that antagonist potency is correlated with a ligand's ability to induce receptor stability (Tm) and crystallogenesis. Using this screening strategy, we solved two structures of NOP in complex with top candidate ligands SB-612111 and C-35. Docking studies indicate that while potent, stabilizing antagonists strongly favor a single binding orientation, less potent ligands can adopt multiple binding modes, contributing to their low Tm values. These results suggest a mechanism for ligand-aided crystallogenesis whereby potent antagonists stabilize a single ligand-receptor conformational pair.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Soluble cytochrome b562,Nociceptin receptor	A, B	424	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 3  Gene Names: cybC, OPRL1 (OOR, ORL1)
Membrane protein mpstruct	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs)	Protein:  Nociceptin/orphanin FQ (N/OFQ) receptor with bound peptide
Find proteins for P0ABE7 (Escherichia coli) Go to UniProtKB:  P0ABE7
Find proteins for P41146 (Homo sapiens) Go to Gene View: OPRL1 Go to UniProtKB:  P41146

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
OLC	B	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate 1-Oleoyl-R-glycerol C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	A, B	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
DGV	A, B	1-benzyl-N-{3-[4-(2,6-dichlorophenyl)piperidin-1-yl]propyl}-D-prolinamide C26 H33 Cl2 N3 O UWHDLFOAIARROU-XMMPIXPASA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DGV	Ki: 0.7 nM (98) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.275 
• R-Value Work: 0.235 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.079	α = 90.00
b = 171.696	β = 103.25
c = 66.491	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PHASER	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-08-30 
• Released Date: 2015-10-21 
• Deposition Author(s): Miller, R.L., Thompson, A.A., Trapella, C., Guerrini, R., Malfacini, D., Patel, N., Han, G.W., Cherezov, V., Calo, G., Katritch, V., Stevens, R.C., GPCR Network (GPCR)

Revision History 

• Version 1.0: 2015-10-21
  Type: Initial release
• Version 1.1: 2015-11-18
  Type: Database references
• Version 1.2: 2015-12-16
  Type: Database references
• Version 1.3: 2016-03-02
  Type: Database references
• Version 1.4: 2017-05-31
  Type: Source and taxonomy
• Version 1.5: 2017-07-05
  Type: Database references