4G3D Transferase date Jul 13, 2012
title Crystal Structure Of Human Nf-Kappab Inducing Kinase (Nik)
authors S.G.Hymowitz, G.De Leon-Boenig
compound source
Molecule: Nf-Kappa-Beta-Inducing Kinase
Chain: A, B, D, E
Synonym: Hsnik, Serinethreonine-Protein Kinase Nik
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Map3k14, Nf-Kappab Inducing Kinase (Nik), Nik
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_vector_type: Baculovirus Transfer Vector
Expression_system_plasmid: Pacgp67
symmetry Space Group: P 21 21 21
R_factor 0.201 R_Free 0.266
length a length b length c angle alpha angle beta angle gamma
45.746 145.851 230.818 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand MG enzyme Transferase E.C. BRENDA
A, D, E, B

Primary referenceThe crystal structure of the catalytic domain of the NF-kappaB inducing kinase reveals a narrow but flexible active site., de Leon-Boenig G, Bowman KK, Feng JA, Crawford T, Everett C, Franke Y, Oh A, Stanley M, Staben ST, Starovasnik MA, Wallweber HJ, Wu J, Wu LC, Johnson AR, Hymowitz SG, Structure. 2012 Oct 10;20(10):1704-14. doi: 10.1016/j.str.2012.07.013. Epub 2012 , Aug 23. PMID:22921830
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (404 Kb) [Save to disk]
  • Biological Unit Coordinates (4g3d.pdb1.gz) 107 Kb
  • Biological Unit Coordinates (4g3d.pdb2.gz) 105 Kb
  • Biological Unit Coordinates (4g3d.pdb3.gz) 99 Kb
  • Biological Unit Coordinates (4g3d.pdb4.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 4G3D
  • CSU: Contacts of Structural Units for 4G3D
  • Structure Factors (502 Kb)
  • Retrieve 4G3D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4G3D from S2C, [Save to disk]
  • Re-refined 4g3d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4G3D 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 4G3D
  • 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 4G3D, from MSDmotif at EBI
  • Fold representative 4g3d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4g3d_A] [4g3d_B] [4g3d_E] [4g3d] [4g3d_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4G3D: [STYKc ] by SMART
  • Other resources with information on 4G3D
  • Community annotation for 4G3D at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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