1GD2 Transcription Dna date Aug 25, 2000
title Crystal Structure Of Bzip Transcription Factor Pap1 Bound To Dna
authors Y.Fujii, T.Shimizu, T.Toda, M.Yanagida, T.Hakoshima
compound source
Molecule: Dna (5'- D(Apgpgptptpapcpgptpapapcpc)-3');
Chain: A, B, C, D
Engineered: Yes
Synthetic: Yes

Molecule: Transcription Factor Pap1
Chain: E, F, G, H, I, J
Fragment: Leucine Zipper Domain
Synonym: Ap-1-Like Transcription Factor
Engineered: Yes

Organism_scientific: Schizosaccharomyces Pombe
Organism_common: Fission Yeast
Organism_taxid: 4896
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a
symmetry Space Group: H 3
R_factor 0.230 R_Free 0.253
length a length b length c angle alpha angle beta angle gamma
240.910 240.910 43.870 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
note 1GD2 is a representative structure
H, F, J, I, G, E

Primary referenceStructural basis for the diversity of DNA recognition by bZIP transcription factors., Fujii Y, Shimizu T, Toda T, Yanagida M, Hakoshima T, Nat Struct Biol 2000 Oct;7(10):889-93. PMID:11017199
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (1gd2.pdb1.gz) 39 Kb
  • Biological Unit Coordinates (1gd2.pdb2.gz) 41 Kb
  • Biological Unit Coordinates (1gd2.pdb3.gz) 8 Kb
  • CSU: Contacts of Structural Units for 1GD2
  • Likely Quarternary Molecular Structure file(s) for 1GD2
  • Structure Factors (468 Kb)
  • Retrieve 1GD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GD2 from S2C, [Save to disk]
  • Re-refined 1gd2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GD2 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 1GD2
  • 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 1GD2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m1gd2, region D:191-248 [Jmol] [rasmolscript] [script source]
        - Domain d1gd2e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1gd2f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1gd2g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1gd2h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1gd2i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1gd2j_, region J [Jmol] [rasmolscript] [script source]
  • Fold representative 1gd2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1gd2_A] [1gd2_D] [1gd2_G] [1gd2_E] [1gd2_C] [1gd2] [1gd2_B] [1gd2_F] [1gd2_H] [1gd2_J] [1gd2_I]
  • SWISS-PROT database: [Q01663]
  • Domain organization of [AP1_SCHPO] by SWISSPFAM
  • Domain found in 1GD2: [BRLZ ] by SMART
  • Other resources with information on 1GD2
  • Community annotation for 1GD2 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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