2DCO Membrane Protein date Jan 11, 2006
title S1p4 First Extracellular Loop Peptidomimetic
authors T.C.T.Pham, R.W.Kriwacki, A.L.Parrill
compound source
Molecule: S1p4 First Extracellular Loop Peptidomimetic
Chain: A
Fragment: Extracellular Loop 1
Synonym: Arfaptin-2, Adp-Ribosylation Factor-Interacting Protein 2, Partner Of Rac1, Protein Por1phingosine 1- Phosphate Receptor Edg-6, S1p Receptor Edg-6, Endothelial Differentiation G-Protein Coupled Receptor 6, Sphingosine 1-Phosphate Receptor 4, S1p4;
Engineered: Yes
Mutation: Yes
Other_details: This Protein Is A Fusion Protein. Residues 13-26 And 29-30 Are From The First Extracellular Loop Of S1p4 Receptor. The Rest, Residues 3-12, 27-28, And 31-34 Are From Arfatin (Pdb Entry 1i49) Segments 139-148, 164- 164, 168-171 Of 1i49 That We Designed To Be In The Sequence.
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: S1p4
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-32a, Cce1a
methodSolution NMR
note 2DCO is a representative structure
Primary referencePeptide design and structural characterization of a GPCR loop mimetic., Pham TC, Kriwacki RW, Parrill AL, Biopolymers. 2007 Jul;86(4):298-310. PMID:17443712
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 2DCO
  • Original NMR restraints for 2DCO from PDB
  • Retrieve 2DCO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DCO from S2C, [Save to disk]
  • View 2DCO 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 2DCO
  • 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
  • 3D motif for 2DCO, from MSDmotif at EBI
  • Fold representative 2dco from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dco] [2dco_A]
  • SWISS-PROT database: [O95977]
  • Domain organization of [S1PR4_HUMAN] by SWISSPFAM
  • Other resources with information on 2DCO
  • Community annotation for 2DCO at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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