5DHG

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

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

  • DOI: 10.1016/j.str.2015.07.024
  • Primary Citation of Related Structures:  

  • 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 iden ...

    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.


    Organizational Affiliation

    Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,Department of Chemical and Pharmaceutical Sciences and LTTA (Laboratorio per le Tecnologie delle Terapie Avanzate), University of Ferrara, 44121 Ferrara, Italy.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA. Electronic address: stevens@usc.edu.,Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Medical Sciences, Section of Pharmacology and National Institute of Neuroscience, University of Ferrara, 44121 Ferrara, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Soluble cytochrome b562,Nociceptin receptor
A, B
424Escherichia coliHomo 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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
B
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
OLA
Query on OLA

Download SDF File 
Download CCD File 
A, B
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
DGV
Query on DGV

Download SDF File 
Download CCD File 
A, B
1-benzyl-N-{3-[4-(2,6-dichlorophenyl)piperidin-1-yl]propyl}-D-prolinamide
C26 H33 Cl2 N3 O
UWHDLFOAIARROU-XMMPIXPASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DGVKi: 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 = 42.079α = 90.00
b = 171.696β = 103.25
c = 66.491γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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