Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.05 kDa 
• Atom Count: 3382 
• Residue Count: 442 
• Unique protein chains: 1

4EJ4

Structure of the delta opioid receptor bound to naltrindole

• DOI: 10.2210/pdb4EJ4/pdb

• Classification: SIGNALING PROTEIN, Hydrolase/Antagonist
• Organism(s): Mus musculus, Escherichia virus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-04-06 Released: 2012-05-16 
• Deposition Author(s): Granier, S., Manglik, A., Kruse, A.C., Kobilka, T.S., Thian, F.S., Weis, W.I., Kobilka, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.282 
• R-Value Work: 0.252 
• R-Value Observed: 0.255 

Literature

Structure of the delta opioid receptor bound to naltrindole

Granier, S., Manglik, A., Kruse, A.C., Kobilka, T.S., Thian, F.S., Weis, W.I., Kobilka, B.K.

(2012) Nature 485: 400-404

• PubMed: 22596164 
• DOI: 10.1038/nature11111
• Primary Citation of Related Structures:  
  4EJ4


• PubMed Abstract: 
  

The opioid receptor family comprises three members, the µ-, δ- and κ-opioid receptors, which respond to classical opioid alkaloids such as morphine and heroin as well as to endogenous peptide ligands like endorphins. They belong to the G-protein-coupled receptor (GPCR) superfamily, and are excellent therapeutic targets for pain control. The δ-opioid receptor (δ-OR) has a role in analgesia, as well as in other neurological functions that remain poorly understood. The structures of the µ-OR and κ-OR have recently been solved. Here we report the crystal structure of the mouse δ-OR, bound to the subtype-selective antagonist naltrindole. Together with the structures of the µ-OR and κ-OR, the δ-OR structure provides insights into conserved elements of opioid ligand recognition while also revealing structural features associated with ligand-subtype selectivity. The binding pocket of opioid receptors can be divided into two distinct regions. Whereas the lower part of this pocket is highly conserved among opioid receptors, the upper part contains divergent residues that confer subtype selectivity. This provides a structural explanation and validation for the 'message-address' model of opioid receptor pharmacology, in which distinct 'message' (efficacy) and 'address' (selectivity) determinants are contained within a single ligand. Comparison of the address region of the δ-OR with other GPCRs reveals that this structural organization may be a more general phenomenon, extending to other GPCR families as well.

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Organizational Affiliation: 

Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Delta-type opioid receptor, Lysozyme chimera	A	461	Mus musculus, Escherichia virus T4	Mutation(s): 3  Gene Names: Oprd1, E EC: 3.2.1.17
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs): Class A	Protein:  δ-opioid receptor in complex with naltrindol
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for P32300 (Mus musculus) Explore P32300  Go to UniProtKB:  P32300

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EJ4	A	(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol C26 H26 N2 O3 WIYUZYBFCWCCQJ-IFKAHUTRSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
EJ4	Ki:  0.3100000023841858   nM  BindingDB
EJ4	Ki:  0.46000000834465027   nM  BindingDB
EJ4	Ki:  0.2199999988079071   nM  BindingDB
EJ4	Ki:  0.20000000298023224   nM  BindingDB
EJ4	Ki:  0.30000001192092896   nM  BindingDB
EJ4	Ki:  0.8999999761581421   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.282 
• R-Value Work: 0.252 
• R-Value Observed: 0.255 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.278	α = 90
b = 73.278	β = 90
c = 266.653	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-06 
• Released Date: 2012-05-16 
Deposition Author(s): Granier, S., Manglik, A., Kruse, A.C., Kobilka, T.S., Thian, F.S., Weis, W.I., Kobilka, B.K.

Revision History 

• Version 1.0: 2012-05-16
  Type: Initial release
  
• Version 1.1: 2012-06-27
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Refinement description, Source and taxonomy