1W9Q Cell Adhesion date Oct 15, 2004
title Crystal Structure Of The Pdz Tandem Of Human Syntenin In Com Tnefaf Peptide
authors J.Grembecka, T.Cierpicki, Y.Devedjiev, D.R.Cooper, 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 Or Mda9 Or Sycl
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgst-Parallel1

Molecule: Tnefaf Peptide
Chain: S
Engineered: Yes
Other_details: Tnefaf

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.174 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.192 72.192 125.887 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 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] (124 Kb) [Save to disk]
  • Biological Unit Coordinates (1w9q.pdb1.gz) 59 Kb
  • Biological Unit Coordinates (1w9q.pdb2.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 1W9Q
  • CSU: Contacts of Structural Units for 1W9Q
  • Likely Quarternary Molecular Structure file(s) for 1W9Q
  • Structure Factors (263 Kb)
  • Retrieve 1W9Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1W9Q from S2C, [Save to disk]
  • Re-refined 1w9q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1W9Q 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 1W9Q
  • 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 1W9Q, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1w9q] [1w9q_A] [1w9q_B] [1w9q_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 1W9Q: [PDZ ] by SMART
  • Other resources with information on 1W9Q
  • Community annotation for 1W9Q 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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