5YHL

Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and an antagonist Br-derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.2 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.333 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Ligand binding to human prostaglandin E receptor EP4at the lipid-bilayer interface.

Toyoda, Y.Morimoto, K.Suno, R.Horita, S.Yamashita, K.Hirata, K.Sekiguchi, Y.Yasuda, S.Shiroishi, M.Shimizu, T.Urushibata, Y.Kajiwara, Y.Inazumi, T.Hotta, Y.Asada, H.Nakane, T.Shiimura, Y.Nakagita, T.Tsuge, K.Yoshida, S.Kuribara, T.Hosoya, T.Sugimoto, Y.Nomura, N.Sato, M.Hirokawa, T.Kinoshita, M.Murata, T.Takayama, K.Yamamoto, M.Narumiya, S.Iwata, S.Kobayashi, T.

(2019) Nat. Chem. Biol. 15: 18-26


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prostaglandin E2 receptor EP4 subtype
A
332Homo sapiensMutation(s): 4 
Gene Names: PTGER4 (PTGER2)
Find proteins for P35408 (Homo sapiens)
Go to Gene View: PTGER4
Go to UniProtKB:  P35408
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of Fab fragment
H
253N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Light chain of Fab fragment
L
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8VL
Query on 8VL

Download SDF File 
Download CCD File 
A
4-[2-[[(2R)-2-(4-bromanylnaphthalen-1-yl)propanoyl]amino]-4-cyano-phenyl]butanoic acid
C24 H21 Br N2 O3
MCJIJRUBPRBSIT-OAHLLOKOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.2 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.333 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 101.970α = 90.00
b = 392.230β = 90.00
c = 81.080γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and Technology AgencyJapan--
Japan Agency for Medical Research and DevelopmentJapan--

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: 2019-01-16
    Type: Data collection, Structure summary
  • Version 1.4: 2019-01-30
    Type: Data collection, Structure summary