1VKX Transcription Dna date Sep 17, 1997
title Crystal Structure Of The Nfkb P50p65 Heterodimer Complexed Immunoglobulin Kb Dna
authors F.Chen, D.B.Huang, G.Ghosh
compound source
Molecule: Dna (5'-D(Tpgpgpgpgpapcptptptpcpc)-3'
Chain: C
Synonym: Immunoglobulin Kappa B Dna
Engineered: Yes
Other_details: Active Nf-Kappa-B Is A Heterodimer Of An Abo Dna-Binding Subunit And The Weak Dna-Binding Subunit P65;
 Synthetic: Yes

Molecule: Dna (5'-D(Apgpgpapapapgptpcpcpcpc)-3'
Chain: D
Synonym: Immunoglobulin Kappa B Dna
Engineered: Yes
Other_details: Active Nf-Kappa-B Is A Heterodimer Of An Abo Dna-Binding Subunit And The Weak Dna-Binding Subunit P65;
Synthetic: Yes

Molecule: Protein (Nf-Kappa B P65 Subunit)
Chain: A
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090

Molecule: Protein (Nf-Kappa B P50 Subunit)
Chain: B
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
symmetry Space Group: P 43 21 2
R_factor 0.208 R_Free 0.320
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.610 106.610 206.560 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
related structures by homologous chain: 1GJI, 1LE5, 1LE9
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceCrystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA., Chen FE, Huang DB, Chen YQ, Ghosh G, Nature 1998 Jan 22;391(6665):410-3. PMID:9450761
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (1vkx.pdb1.gz) 102 Kb
  • CSU: Contacts of Structural Units for 1VKX
  • Likely Quarternary Molecular Structure file(s) for 1VKX
  • Retrieve 1VKX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VKX from S2C, [Save to disk]
    • View 1VKX 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 1VKX
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1VKX, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vkxa2, region A:19-191 [Jmol] [rasmolscript] [script source]
        - Domain d1vkxa1, region A:192-291 [Jmol] [rasmolscript] [script source]
        - Domain d1vkxb2, region B:339-546 [Jmol] [rasmolscript] [script source]
        - Domain d1vkxb1, region B:547-650 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vkx_D] [1vkx_B] [1vkx] [1vkx_A] [1vkx_C]
  • SWISS-PROT database: [P25799] [Q04207]
  • Domain organization of [NFKB1_MOUSE] [TF65_MOUSE] by SWISSPFAM
  • Domain found in 1VKX: [IPT ] by SMART
    • Other resources with information on 1VKX
  • Community annotation for 1VKX at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Domain movements in 1VKX from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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