5YFI

Crystal structure of the anti-human prostaglandin E receptor EP4 antibody Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.848 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
Light chain of Fab fragment
L
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
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.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
H, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.848 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.703α = 90.00
b = 60.784β = 90.00
c = 200.182γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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: 2019-03-06
    Type: Data collection, Database references