6AK3

Crystal structure of the human prostaglandin E receptor EP3 bound to prostaglandin E2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the endogenous agonist-bound prostanoid receptor EP3.

Morimoto, K.Suno, R.Hotta, Y.Yamashita, K.Hirata, K.Yamamoto, M.Narumiya, S.Iwata, S.Kobayashi, T.

(2019) Nat. Chem. Biol. 15: 8-10


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prostaglandin E2 receptor EP3 subtype,Soluble cytochrome b562
B, A
418Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 9 
Gene Names: cybC, PTGER3
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
prostanoid receptor EP3 with bound PGE2
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P43115 (Homo sapiens)
Go to Gene View: PTGER3
Go to UniProtKB:  P43115
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P2E
Query on P2E

Download SDF File 
Download CCD File 
A, B
(Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid
Prostaglandin E2
C20 H32 O5
XEYBRNLFEZDVAW-ARSRFYASSA-N
 Ligand Interaction
POV
Query on POV

Download SDF File 
Download CCD File 
A, B
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
POPC
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.090α = 90.00
b = 42.280β = 96.09
c = 161.300γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP18gm0910007
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101079

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Structure summary
  • Version 1.2: 2018-12-19
    Type: Data collection, Database references
  • Version 1.3: 2019-01-30
    Type: Data collection, Database references