3BBB Transferase date Nov 09, 2007
title Crystal Structure Of The Nm23-H2 Transcription Factor Comple Dinucleotide D(Ag)
authors A.Weichsel, W.R.Montfort
compound source
Molecule: Nucleoside Diphosphate Kinase B
Chain: A, B, C, D, E, F
Synonym: Ndk B, Ndp Kinase B, Nm23-H2, C-Myc Purine-Binding Transcription Factor Puf;
Ec: 2.7.4.6
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nme2, Nm23b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_plasmid: Plasmid
symmetry Space Group: P 21 21 21
R_factor 0.175 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.466 118.219 128.910 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.30 Å
ligand DA, DG enzyme Transferase E.C.2.7.4.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B
  • protein histidine kinase act...


  • Primary referenceNM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1., Dexheimer TS, Carey SS, Zuohe S, Gokhale VM, Hu X, Murata LB, Maes EM, Weichsel A, Sun D, Meuillet EJ, Montfort WR, Hurley LH, Mol Cancer Ther. 2009 May 12. PMID:19435876
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (328 Kb) [Save to disk]
  • Biological Unit Coordinates (3bbb.pdb1.gz) 323 Kb
  • LPC: Ligand-Protein Contacts for 3BBB
  • CSU: Contacts of Structural Units for 3BBB
  • Likely Quarternary Molecular Structure file(s) for 3BBB
  • Structure Factors (2833 Kb)
  • Retrieve 3BBB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BBB from S2C, [Save to disk]
  • Re-refined 3bbb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BBB 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 3BBB
  • 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 3BBB, from MSDmotif at EBI
  • Fold representative 3bbb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bbb_F] [3bbb] [3bbb_B] [3bbb_D] [3bbb_E] [3bbb_C] [3bbb_A]
  • SWISS-PROT database: [P22392]
  • Domain organization of [NDKB_HUMAN] by SWISSPFAM
  • Domain found in 3BBB: [NDK ] by SMART
  • Other resources with information on 3BBB
  • Community annotation for 3BBB 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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