4DN5 Transferase date Feb 08, 2012
title Crystal Structure Of Nf-Kb-Inducing Kinase (Nik)
authors X.Min, J.Liu, A.Sudom, N.P.Walker, Z.Wang
compound source
Molecule: Mitogen-Activated Protein Kinase Kinase Kinase 14
Chain: A, B
Fragment: Unp Residues 330-680
Synonym: Nf-Kappa-Beta-Inducing Kinase, Hsnik, Serinethreo Protein Kinase Nik;
Ec: 2.7.11.25
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Map3k14, Nf-Kb-Inducing Kinase, Nik
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfastbacht
symmetry Space Group: P 41
R_factor 0.182 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.060 85.060 115.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand AGS, EDO, GOL, MG enzyme Transferase E.C.2.7.11.25 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure of the nuclear factor kappaB-inducing kinase (NIK) kinase domain reveals a constitutively active conformation., Liu J, Sudom A, Min X, Cao Z, Gao X, Ayres M, Lee F, Cao P, Johnstone S, Plotnikova O, Walker N, Chen G, Wang Z, J Biol Chem. 2012 Aug 10;287(33):27326-34. Epub 2012 Jun 20. PMID:22718757
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (114 Kb) [Save to disk]
  • Biological Unit Coordinates (4dn5.pdb1.gz) 56 Kb
  • Biological Unit Coordinates (4dn5.pdb2.gz) 55 Kb
  • Biological Unit Coordinates (4dn5.pdb3.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 4DN5
  • CSU: Contacts of Structural Units for 4DN5
  • Structure Factors (1094 Kb)
  • Retrieve 4DN5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DN5 from S2C, [Save to disk]
  • Re-refined 4dn5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DN5 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 4DN5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4DN5, from MSDmotif at EBI
  • Fold representative 4dn5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dn5] [4dn5_A] [4dn5_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4DN5: [STYKc ] by SMART
  • Other resources with information on 4DN5
  • Community annotation for 4DN5 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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