1OBZ Cell Adhesion date Jan 31, 2003
title Crystal Structure Of The Complex Of The Pdz Tandem Of Synten Interleukin 5 Receptor Alpha Peptide.
authors B.S.Kang, D.R.Cooper, Y.Devedjiev, U.Derewenda, Z.S.Derewenda
compound source
Molecule: Syntenin 1
Chain: A, B
Fragment: Pdz2, Residues 113-273
Synonym: Syndecan Binding Protein 1, Melanoma Differentiati Associated Protein-9, Mda-9, Scaffold Protein Pbp1, Tacip18 Alpha Cytoplasmic Domain-Interacting Protein 18;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Atcc: 72537
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector: Pgst-Parallel1

Molecule: Interleukin 5 Receptor Alpha
Chain: P
Fragment: Last 8 Residues, Residues 413-420
Synonym: Il-5r-Alpha, Cd125 Antigen
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.148 R_Free 0.213
length a length b length c angle alpha angle beta angle gamma
101.485 48.172 74.996 90.00 120.24 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand ACT enzyme
related structures by homologous chain: 1OBX, 1V1T
A, B

Primary referenceMolecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm., Kang BS, Cooper DR, Devedjiev Y, Derewenda U, Derewenda ZS, Structure (Camb) 2003 Jul;11(7):845-53. PMID:12842047
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (119 Kb) [Save to disk]
  • Biological Unit Coordinates (1obz.pdb1.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 1OBZ
  • CSU: Contacts of Structural Units for 1OBZ
  • Likely Quarternary Molecular Structure file(s) for 1OBZ
  • Structure Factors (458 Kb)
  • Retrieve 1OBZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1OBZ from S2C, [Save to disk]
  • Re-refined 1obz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1OBZ 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 1OBZ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1OBZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1obza1, region A:111-194 [Jmol] [rasmolscript] [script source]
        - Domain d1obza2, region A:195-273 [Jmol] [rasmolscript] [script source]
        - Domain d1obzb1, region B:108-194 [Jmol] [rasmolscript] [script source]
        - Domain d1obzb2, region B:195-272 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1obz_P] [1obz_A] [1obz_B] [1obz]
  • SWISS-PROT database: [Q01344] [O00560]
  • Belongs to the ezrin/radixin/moesin-binding phosphoprotein 50 (ebp50) family according to TCDB.
  • Domain organization of [IL5RA_HUMAN] [SDCB1_HUMAN] by SWISSPFAM
  • Domain found in 1OBZ: [PDZ ] by SMART
  • Other resources with information on 1OBZ
  • Community annotation for 1OBZ 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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