4RWD

XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for bifunctional peptide recognition at human delta-opioid receptor.

Fenalti, G.Zatsepin, N.A.Betti, C.Giguere, P.Han, G.W.Ishchenko, A.Liu, W.Guillemyn, K.Zhang, H.James, D.Wang, D.Weierstall, U.Spence, J.C.Boutet, S.Messerschmidt, M.Williams, G.J.Gati, C.Yefanov, O.M.White, T.A.Oberthuer, D.Metz, M.Yoon, C.H.Barty, A.Chapman, H.N.Basu, S.Coe, J.Conrad, C.E.Fromme, R.Fromme, P.Tourwe, D.Schiller, P.W.Roth, B.L.Ballet, S.Katritch, V.Stevens, R.C.Cherezov, V.

(2015) Nat.Struct.Mol.Biol. 22: 265-268

  • DOI: 10.1038/nsmb.2965
  • Primary Citation of Related Structures:  4RWA

  • PubMed Abstract: 
  • Bifunctional μ- and δ-opioid receptor (OR) ligands are potential therapeutic alternatives, with diminished side effects, to alkaloid opiate analgesics. We solved the structure of human δ-OR bound to the bifunctional δ-OR antagonist and μ-OR agonist t ...

    Bifunctional μ- and δ-opioid receptor (OR) ligands are potential therapeutic alternatives, with diminished side effects, to alkaloid opiate analgesics. We solved the structure of human δ-OR bound to the bifunctional δ-OR antagonist and μ-OR agonist tetrapeptide H-Dmt-Tic-Phe-Phe-NH2 (DIPP-NH2) by serial femtosecond crystallography, revealing a cis-peptide bond between H-Dmt and Tic. The observed receptor-peptide interactions are critical for understanding of the pharmacological profiles of opioid peptides and for development of improved analgesics.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Soluble cytochrome b562,Delta-type opioid receptor
A, B
411Escherichia coliHomo sapiens
This entity is chimeric
Gene Names: cybC, OPRD1 (OPRD)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
δ-opioid receptor in complex with naltrindol
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P41143 (Homo sapiens)
Go to Gene View: OPRD1
Go to UniProtKB:  P41143
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
bifunctional peptide
G, H
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-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
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001256
Query on PRD_001256
G,Hbifunctional peptidePeptide-like / Unknown

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 156.230α = 90.00
b = 89.290β = 92.30
c = 96.420γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Database references
  • Version 1.2: 2017-06-07
    Type: Database references, Structure summary
  • Version 1.3: 2018-02-14
    Type: Data collection