4GVD Signaling Protein date Aug 30, 2012
title Crystal Structure Of T-Cell Lymphoma Invasion And Metastasis Complex With Syndecan1 Peptide
authors X.Liu, T.R.Shepherd, A.M.Murray, Z.Xu, E.J.Fuentes
compound source
Molecule: T-Lymphoma Invasion And Metastasis-Inducing Prote
Chain: A, B
Fragment: Pdz Domain (Unp Residues 841-930)
Synonym: Tiam-1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Human
Gene: Tiam1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a-6his-Rtev

Molecule: Syndecan-1
Chain: C, D
Fragment: Unp Residues 303-310
Synonym: Synd1
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.196 R_Free 0.243
length a length b length c angle alpha angle beta angle gamma
26.517 58.106 50.948 90.00 90.50 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand ANS, CL, NA enzyme
A, B

Primary referenceThe structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics., Liu X, Shepherd TR, Murray AM, Xu Z, Fuentes EJ, Structure. 2013 Mar 5;21(3):342-54. doi: 10.1016/j.str.2013.01.004. Epub 2013 Feb, 7. PMID:23395182
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (37 Kb) [Save to disk]
  • Biological Unit Coordinates (4gvd.pdb1.gz) 17 Kb
  • Biological Unit Coordinates (4gvd.pdb2.gz) 18 Kb
  • LPC: Ligand-Protein Contacts for 4GVD
  • CSU: Contacts of Structural Units for 4GVD
  • Structure Factors (525 Kb)
  • Retrieve 4GVD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GVD from S2C, [Save to disk]
  • Re-refined 4gvd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GVD 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 4GVD
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4GVD, from MSDmotif at EBI
  • Fold representative 4gvd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gvd] [4gvd_C] [4gvd_B] [4gvd_A] [4gvd_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4GVD: [PDZ ] by SMART
  • Other resources with information on 4GVD
  • Community annotation for 4GVD at PDBWiki (http://pdbwiki.org)

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