4RWD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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, 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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Soluble cytochrome b562,Delta-type opioid receptorA, B411Escherichia 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
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P41143
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
bifunctional peptideC [auth G],
D [auth H]
5synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DI7
Query on DI7
C [auth G],
D [auth H]
L-PEPTIDE LINKINGC11 H15 N O3TYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001256
Query on PRD_001256
C [auth G], D [auth H]bifunctional peptidePeptide-like / Unknown Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.23α = 90
b = 89.29β = 92.3
c = 96.42γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
CrystFELdata reduction
CrystFELdata 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: 2018-02-14
    Changes: Data collection