5YHL Signaling Protein Immune System date Sep 28, 2017
title Crystal Structure Of The Human Prostaglandin E Receptor Ep4 With Fab And An Antagonist Br-Derivative
authors Y.Toyoda, K.Morimoto, R.Suno, S.Horita, S.Iwata, T.Kobayashi
compound source
Molecule: Prostaglandin E2 Receptor Ep4 Subtype
Chain: A
Fragment: Unp Residues 4-217, 260-366
Synonym: Pge2 Receptor Ep4 Subtype,Prostanoid Ep4 Receptor
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ptger4, Ptger2
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108

Molecule: Heavy Chain Of Fab Fragment
Chain: H
Synonym: Fabh
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Hybrid
Expression_system_taxid: 37965

Molecule: Light Chain Of Fab Fragment
Chain: L
Synonym: Fabl
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Hybrid
Expression_system_taxid: 37965
symmetry Space Group: C 2 2 21
R_factor 0.333 R_Free 0.359
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.970 392.230 81.080 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.20 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceLigand binding to human prostaglandin E receptor EP4 at 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, Nat Chem Biol. 2019 Jan;15(1):18-26. doi: 10.1038/s41589-018-0131-3. Epub 2018, Dec 3. PMID:30510193
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (121 Kb) [Save to disk]
  • Biological Unit Coordinates (5yhl.pdb1.gz) 116 Kb
  • CSU: Contacts of Structural Units for 5YHL
  • Structure Factors (697 Kb)
  • Retrieve 5YHL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YHL from S2C, [Save to disk]
  • View 5YHL in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5YHL
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5yhl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yhl_A] [5yhl_L] [5yhl_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YHL
  • Community annotation for 5YHL at PDBWiki (http://pdbwiki.org)

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