4N6H

1.8 A Structure of the human delta opioid 7TM receptor (PSI Community Target)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.172

Literature

Macromolecules
Sequence Display for 4N6H

Classification: SIGNALING PROTEIN

Total Structure Weight: 52088.92

Macromolecule Entities
Molecule Chains Length Organism Details
Soluble cytochrome b562, Delta-type opioid receptor chimeric protein A 414 Escherichia coli Homo sapiens Fragment: UNP P0ABE7 residues 23-128, UNP P41143 residues 36-338
Mutation: M1007W, H1102I, R1106L, P37S
Gene Name(s): cybC OPRD1 Gene View OPRD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: δ-opioid receptor in complex with naltrindol


Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EJ4
Query on 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
Naltrindole (Synonym)
C26 H26 N2 O3
WIYUZYBFCWCCQJ-IFKAHUTRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OLC
Query on OLC

A (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol (Synonym)
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OLA
Query on OLA

A OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

A TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TLA
Query on TLA

A L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
EJ4 Ki: 0.03 - 2.63 nM (98 - 99) BindingDB

N/A in BindingMoad
Kd: 0.52 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.172
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 86.23 α = 90.00
b = 72.85 β = 107.48
c = 84.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-10-12
  • Released Date: 2013-12-25
  • Deposition author(s): Fenalti, G., Giguere, P.M., Katritch, V., Huang, X.-P., Thompson, A.A., Han, G.W., Cherezov, V., Roth, B.L., Stevens, R.C., GPCR Network (GPCR)

Revision History

  • 2014-03-05
    Type: Entry title | Details: --
  • 2014-03-05
    Type: Citation | Details: Citation update
  • 2014-01-08
    Type: Citation | Details: Citation update