4GEI Protein Binding date Aug 02, 2012
title N-Terminal Domain Of Vdup-1
authors G.Polekhina, S.F.Kok, D.B.Ascher, M.Waltham
compound source
Molecule: Thioredoxin-Interacting Protein
Chain: A
Fragment: N-Terminal Domain, Unp Residues 2-149
Synonym: Thioredoxin-Binding Protein 2, Vitamin D3 Up-Regul Protein 1;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Txnip, Vdup1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ec538
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pmcsg7
symmetry Space Group: C 1 2 1
R_factor 0.180 R_Free 0.203
length a length b length c angle alpha angle beta angle gamma
98.250 76.280 31.030 90.00 92.65 90.00
method X-Ray Diffractionresolution 1.50 Å
Primary referenceStructure of the N-terminal domain of human thioredoxin-interacting protein., Polekhina G, Ascher DB, Kok SF, Beckham S, Wilce M, Waltham M, Acta Crystallogr D Biol Crystallogr. 2013 Mar;69(Pt 3):333-44. doi:, 10.1107/S0907444912047099. Epub 2013 Feb 16. PMID:23519408
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (4gei.pdb1.gz) 32 Kb
  • CSU: Contacts of Structural Units for 4GEI
  • Structure Factors (490 Kb)
  • Retrieve 4GEI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GEI from S2C, [Save to disk]
  • Re-refined 4gei structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GEI 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 4GEI
  • 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 4GEI, from MSDmotif at EBI
  • Fold representative 4gei from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gei_A] [4gei]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4GEI
  • Community annotation for 4GEI at PDBWiki (http://pdbwiki.org)

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