5YHL

Anomalous bromine signal of the human prostaglandin E receptor EP4 in complex with Fab and ONO-AE3-208-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 1.1 of the entry. See complete history

Literature

Ligand binding to human prostaglandin E receptor EP4 at the lipid-bilayer interface

Toyoda, Y.Morimoto, K.Suno, R.Horita, S.Iwata, S.Kobayashi, T.

(2018) Nat.Chem.Biol. --: --


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
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXphasing
XDSdata reduction
PHENIXrefinement

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