3A4R Transcription date Jul 14, 2009
title The Crystal Structure Of Sumo-Like Domain 2 In Nip45
authors N.Sekiyama, K.Arita, Y.Ikeda, M.Ariyoshi, H.Tochio, H.Saitoh, M.Shirakawa
compound source
Molecule: Nfatc2-Interacting Protein
Chain: A, B
Fragment: Sld2, Ubiquitin-Like Domain, Residues 339-412
Synonym: Nip45, Nuclear Factor Of Activated T-Cells, Cytoplasmic 2-Interacting Protein, 45 Kda Nf-At-Interacting Protein, 45 Kda Nfat-Interacting Protein;
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Nip45
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p
symmetry Space Group: P 1 21 1
R_factor 0.158 R_Free 0.184
crystal
cell
length a length b length c angle alpha angle beta angle gamma
26.953 35.373 68.943 90.00 97.18 90.00
method X-Ray Diffractionresolution 1.00 Å
ligand EDO, SO4 enzyme
note 3A4R is a representative structure
Primary referenceStructural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45., Sekiyama N, Arita K, Ikeda Y, Hashiguchi K, Ariyoshi M, Tochio H, Saitoh H, Shirakawa M, Proteins. 2009 Dec 4. PMID:20077568
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (3a4r.pdb1.gz) 43 Kb
  • Biological Unit Coordinates (3a4r.pdb2.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 3A4R
  • CSU: Contacts of Structural Units for 3A4R
  • Structure Factors (435 Kb)
  • Retrieve 3A4R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A4R from S2C, [Save to disk]
  • Re-refined 3a4r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A4R 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 3A4R
  • 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 3A4R, from MSDmotif at EBI
  • Fold representative 3a4r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a4r] [3a4r_B] [3a4r_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3A4R
  • Community annotation for 3A4R 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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