1V1T Cell Adhesion date Apr 23, 2004
title Crystal Structure Of The Pdz Tandem Of Human Syntenin In Com Tneykv 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 108-273
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
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgst-Parallel1
Other_details: Gene, Sdcbp Or Mda9 Or Sycl

Molecule: Tneykv Peptide
Chain: S, T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.181 R_Free 0.229
length a length b length c angle alpha angle beta angle gamma
72.341 72.341 125.676 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand BEZ enzyme
related structures by homologous chain: 1OBY, 1OBZ
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] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (1v1t.pdb1.gz) 117 Kb
  • LPC: Ligand-Protein Contacts for 1V1T
  • CSU: Contacts of Structural Units for 1V1T
  • Likely Quarternary Molecular Structure file(s) for 1V1T
  • Structure Factors (241 Kb)
  • Retrieve 1V1T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1V1T from S2C, [Save to disk]
  • Re-refined 1v1t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1V1T 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 1V1T
  • 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 1V1T, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1v1t] [1v1t_S] [1v1t_B] [1v1t_A] [1v1t_T]
  • 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 1V1T: [PDZ ] by SMART
  • Other resources with information on 1V1T
  • Community annotation for 1V1T at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science