1W9O Cell Adhesion date Oct 15, 2004
title Crystal Structure Of The Pdz Tandem Of Human Syntenin In Com Tneyyv Peptide
authors J.Grembecka, T.Cierpicki, Y.Devedjiev, D.R.Cooper, U.Derewenda, Z.S.Derewenda
compound source
Molecule: Syntenin 1
Chain: A, B
Fragment: Pdz Tandem, Residues 113-273
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, Mda9, Sycl
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgst-Parallel1

Molecule: Tneyyv Peptide
Chain: S, T
Engineered: Yes
Other_details: Tneyyv

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.214 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.134 72.134 126.221 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand BEZ enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe binding of the PDZ tandem of syntenin to target proteins., Grembecka J, Cierpicki T, Devedjiev Y, Derewenda U, Kang BS, Bushweller JH, Derewenda ZS, Biochemistry. 2006 Mar 21;45(11):3674-83. PMID:16533050
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk]
  • Biological Unit Coordinates (1w9o.pdb1.gz) 29 Kb
  • Biological Unit Coordinates (1w9o.pdb2.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 1W9O
  • CSU: Contacts of Structural Units for 1W9O
  • Likely Quarternary Molecular Structure file(s) for 1W9O
  • Structure Factors (119 Kb)
  • Retrieve 1W9O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1W9O from S2C, [Save to disk]
  • Re-refined 1w9o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1W9O 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 1W9O
  • 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 1W9O, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1w9o_A] [1w9o_T] [1w9o] [1w9o_B] [1w9o_S]
  • 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 1W9O: [PDZ ] by SMART
  • Other resources with information on 1W9O
  • Community annotation for 1W9O 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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