Synchrotron structure of the human delta opioid receptor in complex with a bifunctional peptide (PSI community target)

Experimental Data Snapshot

  • Resolution: 3.28 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

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This is version 1.5 of the entry. See complete history


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: https://doi.org/10.1038/nsmb.2965
  • Primary Citation of Related Structures:  
    4RWA, 4RWD

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Delta-type opioid receptor
A, B
411Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: cybCOPRDOPRD1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41143 (Homo sapiens)
Explore P41143 
Go to UniProtKB:  P41143
PHAROS:  P41143
GTEx:  ENSG00000116329 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P41143
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
bifunctional peptideC [auth G],
D [auth H]
5synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OLC

Download Ideal Coordinates CCD File 
E [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on DI7
C [auth G],
D [auth H]
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 3.28 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.549α = 90
b = 86.121β = 92.21
c = 94.684γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2017-06-07
    Changes: Database references, Structure summary
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-12-06
    Changes: Data collection, Derived calculations