1GD2	Transcription Dna	date	Aug 25, 2000
title	Crystal Structure Of Bzip Transcription Factor Pap1 Bound To
authors	Y.Fujii, T.Shimizu, T.Toda, M.Yanagida, T.Hakoshima
compound		source
Molecule: Dna (5'-D(Apgpgptptpapcpgptpapapcpc) 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
crystal cell	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 Diffraction	resolution	2.00 Å
note	1GD2 is a representative structure
Gene Ontology	Chain Function Process Component H, F, J, I, G, E
Primary reference	Structural 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] (90 Kb) [Save to disk] Biological Unit Coordinates (1gd2.pdb1.gz) 39 Kb Biological Unit Coordinates (1gd2.pdb2.gz) 40 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

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 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] 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)

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