1VA2 Transcription date Feb 07, 2004
title Solution Structure Of Transcription Factor Sp1 Dna Binding D (Zinc Finger 2)
authors S.Oka, Y.Shiraishi, T.Yoshida, T.Ohkubo, Y.Sugiura, Y.Kobayashi
compound source
Molecule: Transcription Factor Sp1
Chain: A
Fragment: Zinc Finger 2
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sp1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pevsp1
methodSolution NMR
ligand ZN enzyme
related structures by homologous chain: 1MEY
Primary referenceNMR structure of transcription factor Sp1 DNA binding domain., Oka S, Shiraishi Y, Yoshida T, Ohkubo T, Sugiura Y, Kobayashi Y, Biochemistry 2004 Dec 28;43(51):16027-35. PMID:15609997
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (268 Kb) [Save to disk]
  • Biological Unit Coordinates (1va2.pdb1.gz) 9 Kb
  • LPC: Ligand-Protein Contacts for 1VA2
  • CSU: Contacts of Structural Units for 1VA2
  • Original NMR restraints for 1VA2 from PDB
  • Retrieve 1VA2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VA2 from S2C, [Save to disk]
    • View 1VA2 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 1VA2
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1VA2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n1va2, region A:1-406 [Jmol] [rasmolscript] [script source]
        - Domain d1s1va2, region A:1-429 [Jmol] [rasmolscript] [script source]
        - Domain d1u1va2, region A:129-278 [Jmol] [rasmolscript] [script source]
        - Domain d1h1va2, region A:147-375 [Jmol] [rasmolscript] [script source]
        - Domain d1f1va2, region A:148-323 [Jmol] [rasmolscript] [script source]
        - Domain d1a1va2, region A:326-624 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1va2] [1va2_A]
  • SWISS-PROT database: [P08047]
  • Domain organization of [SP1_HUMAN] by SWISSPFAM
  • Domain found in 1VA2: [ZnF_C2H2 ] by SMART
    • Other resources with information on 1VA2
  • Community annotation for 1VA2 at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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