This website does readability filtering of other pages. All styles, scripts, forms and ads are stripped. If you want your website excluded or have other feedback, use this form.

RCSB PDB - 4RWD: XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide

162529 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education


Asymmetric Unit

&nbsp3D View:&nbspStructure | Electron Density | Ligand Interaction


Standalone Viewers &nbsp
Protein Workshop | Ligand Explorer


Global Symmetry: Cyclic - C2&nbsp&nbsp(3D View)
Global Stoichiometry: Hetero 4-mer -&nbspA2,B2&nbsp
Pseudo Symmetry: Asymmetric - C1&nbsp
Pseudo Stoichiometry: Hetero 4-mer -Hetero 4-mer&nbsp Biological Assembly 1 &nbsp

&nbsp3D View:&nbspStructure | Electron Density | Ligand Interaction


Standalone Viewers &nbsp
Protein Workshop | Ligand Explorer


Global Symmetry: Asymmetric - C1&nbsp
Global Stoichiometry: Hetero 2-mer -&nbspA1B&nbsp
Find Similar Assemblies

Biological assembly 1&nbspgenerated by PISA (software)

Biological Assembly 2 &nbsp

&nbsp3D View:&nbspStructure | Electron Density | Ligand Interaction


Standalone Viewers &nbsp
Protein Workshop | Ligand Explorer


Global Symmetry: Asymmetric - C1&nbsp
Global Stoichiometry: Hetero 2-mer -&nbspA1B&nbsp
Find Similar Assemblies

Biological assembly 2&nbspgenerated by PISA (software)

PreviousNext

Macromolecule Content

  • Total Structure Weight: 95.69&nbsp
  • Atom Count: 6326&nbsp
  • Residue Count: 811&nbsp
  • Unique protein chains: 2

4RWD

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


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.70 Å
  • R-Value Free:&nbsp0.238&nbsp
  • R-Value Work:&nbsp0.208&nbsp
  • R-Value Observed:&nbsp0.210&nbsp

wwPDB Validation&nbsp3D Report&nbspFull Report


This is version 1.3 of the entry. See complete&nbsphistory.&nbsp

Literature

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

Fenalti, G.,&nbspZatsepin, N.A.,&nbspBetti, C.,&nbspGiguere, P.,&nbspHan, G.W.,&nbspIshchenko, A.,&nbspLiu, W.,&nbspGuillemyn, K.,&nbspZhang, H.,&nbspJames, D.,&nbspWang, D.,&nbspWeierstall, U.,&nbspSpence, J.C.,&nbspBoutet, S.,&nbspMesserschmidt, M.,&nbspWilliams, G.J.,&nbspGati, C.,&nbspYefanov, O.M.,&nbspWhite, T.A.,&nbspOberthuer, D.,&nbspMetz, M.,&nbspYoon, C.H.,&nbspBarty, A.,&nbspChapman, H.N.,&nbspBasu, S.,&nbspCoe, J.,&nbspConrad, C.E.,&nbspFromme, R.,&nbspFromme, P.,&nbspTourwe, D.,&nbspSchiller, P.W.,&nbspRoth, B.L.,&nbspBallet, S.,&nbspKatritch, V.,&nbspStevens, R.C.,&nbspCherezov, V.

(2015) Nat Struct Mol Biol&nbsp22: 265-268

  • PubMed:&nbsp25686086&nbspSearch on PubMedSearch on PubMed Central
  • DOI:&nbsp10.1038/nsmb.2965
  • Structures With Same Primary Citation

  • PubMed Abstract:&nbsp
  • 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:&nbsp

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



Macromolecules

Find similar proteins by:&nbspSequence&nbsp | &nbspStructure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails Soluble cytochrome b562,Delta-type opioid receptor A, B 411 Escherichia coli,&nbspHomo sapiens
This entity is chimeric Mutation(s): 3&nbsp
Gene Names:&nbspcybC
Membrane protein
Mpstruc Group:&nbsp
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL Sub Group:&nbsp
G Protein-Coupled Receptors (GPCRs) Protein:&nbsp
δ-opioid receptor with bound antagonist/agonist tetrapeptide DIPP-NH2 Find proteins for&nbspP0ABE7&nbsp(Escherichia coli) Go to UniProtKB: &nbspP0ABE7
  • Protein Feature View
Full Protein Feature View for&nbspP0ABE7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails bifunctional peptide G, H 5 synthetic construct Mutation(s): 0&nbsp
Protein Feature View is not available: No corresponding UniProt sequence found. Small Molecules Ligands&nbsp3 Unique IDChainsName / Formula / InChI Key2D Diagram3D Interactions OLC
Query on OLC

Download CCD File&nbsp A, B (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N  Ligand Interaction OLA
Query on OLA

Download CCD File&nbsp A, B OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N  Ligand Interaction NA
Query on NA

Download CCD File&nbsp A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N  Ligand Interaction Biologically Interesting Molecules&nbsp1 Unique IDChainsNameType/Class2D Diagram3D Interactions PRD_001256
Query on PRD_001256 G, H bifunctional peptide Peptide-like&nbsp/&nbsp Unknown

--

Modified Residues&nbsp 1 Unique IDChainsTypeFormula2D DiagramParent DI7
Query on DI7 G,H L-PEPTIDE LINKING C11 H15 N O3 TYR Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.70 Å
  • R-Value Free:&nbsp0.238&nbsp
  • R-Value Work:&nbsp0.208&nbsp
  • R-Value Observed:&nbsp0.210&nbsp
  • Space Group:&nbspC 1 2 1
Unit Cell:Length ( Å )Angle ( ˚ )a = 156.23 α = 90 b = 89.29 β = 92.3 c = 96.42 γ = 90 Software Package:Software NamePurposePHASER phasing REFMAC refinement CrystFEL data reduction CrystFEL data scaling

Structure Validation

View&nbspFull Validation Report


View more in-depth experimental data
Entry History&nbsp

Deposition Data

Revision History&nbsp

  • 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

RCSB PDB (citation) is hosted by

RCSB PDB is a member of the

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.