1R6J Membrane Protein date Oct 15, 2003
title Ultrahigh Resolution Crystal Structure Of Syntenin Pdz2
authors B.S.Kang, Y.Devedjiev, U.Derewenda, Z.S.Derewenda
compound source
Molecule: Syntenin 1
Chain: A
Fragment: Pdz2 Domain (Residues 197-273)
Synonym: Syndecan Binding Protein 1, Melanoma Differentiati Associated Protein-9, Mda-9, Scaffold Protein Pbp1, Pro-Tgf Cytoplasmic Domain-Interacting Protein 18, Tacip18;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sdcbp Or Mda9 Or Sycl
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgst-Parallel1
symmetry Space Group: P 1 21 1
length a length b length c angle alpha angle beta angle gamma
25.876 39.544 32.276 90.00 109.64 90.00
method X-Ray Diffractionresolution 0.73 Å
ligand CL enzyme
note 1R6J is a representative structure
related structures by homologous chain: 1NTE

Primary referenceThe PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography., Kang BS, Devedjiev Y, Derewenda U, Derewenda ZS, J Mol Biol 2004 Apr 30;338(3):483-93. PMID:15081807
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (1r6j.pdb1.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 1R6J
  • CSU: Contacts of Structural Units for 1R6J
  • Likely Quarternary Molecular Structure file(s) for 1R6J
  • Structure Factors (779 Kb)
  • Retrieve 1R6J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1R6J from S2C, [Save to disk]
  • Re-refined 1r6j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1R6J 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 1R6J
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1R6J from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1R6J, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1r6ja_, region A [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1r6j_A] [1r6j]
  • SWISS-PROT database: [O00560]
  • Belongs to the ezrin/radixin/moesin-binding phosphoprotein 50 (ebp50) family according to TCDB.
  • Domain organization of [SDCB1_HUMAN] by SWISSPFAM
  • Domain found in 1R6J: [PDZ ] by SMART
  • Other resources with information on 1R6J
  • Community annotation for 1R6J 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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