2PF5 Cell Adhesion date Apr 04, 2007
title Crystal Structure Of The Human Tsg-6 Link Module
authors V.A.Higman, D.J.Mahoney, M.E.M.Noble, A.J.Day
compound source
Molecule: Tumor Necrosis Factor-Inducible Protein Tsg-6
Chain: A, B, C, D, E
Fragment: Link_module, Residues 36-133 In Preprotein
Synonym: Tnf- Stimulated Gene 6 Protein; Hyaluronate-Bindin
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfaip6, Tsg6
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet
Expression_system_plasmid: Prk172
Other_details: See Day Et Al. (1996) Protein Expression & Purification 8, 1-16.
symmetry Space Group: C 1 2 1
R_factor 0.194 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.816 75.870 90.674 90.00 103.42 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 2PE, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, E, B


Primary referencePlasticity of the TSG-6 HA-binding loop and mobility in the TSG-6-HA complex revealed by NMR and X-ray crystallography., Higman VA, Blundell CD, Mahoney DJ, Redfield C, Noble ME, Day AJ, J Mol Biol. 2007 Aug 17;371(3):669-84. Epub 2007 Jun 2. PMID:17585936
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (2pf5.pdb1.gz) 18 Kb
  • Biological Unit Coordinates (2pf5.pdb2.gz) 20 Kb
  • Biological Unit Coordinates (2pf5.pdb3.gz) 18 Kb
  • Biological Unit Coordinates (2pf5.pdb4.gz) 21 Kb
  • Biological Unit Coordinates (2pf5.pdb5.gz) 17 Kb
  • LPC: Ligand-Protein Contacts for 2PF5
  • CSU: Contacts of Structural Units for 2PF5
  • Likely Quarternary Molecular Structure file(s) for 2PF5
  • Structure Factors (1040 Kb)
  • Retrieve 2PF5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PF5 from S2C, [Save to disk]
  • Re-refined 2pf5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PF5 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 2PF5
  • 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 2PF5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pf5] [2pf5_A] [2pf5_C] [2pf5_B] [2pf5_E] [2pf5_D]
  • SWISS-PROT database: [P98066]
  • Domain organization of [TSG6_HUMAN] by SWISSPFAM
  • Domain found in 2PF5: [LINK ] by SMART
  • Other resources with information on 2PF5
  • Community annotation for 2PF5 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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