1YTB Transcription Dna date Sep 28, 1994
title Crystal Structure Of A Yeast Tbptata-Box Complex
authors Y.Kim, J.H.Geiger, S.Hahn, P.B.Sigler
compound source
Molecule: Dna (29mer)
Chain: C, D
Engineered: Yes
 Synthetic: Yes

Molecule: Protein (Tata Binding Protein (Tbp))
Chain: A, B
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43
R_factor 0.201 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.770 100.770 66.500 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
note 1YTB (Molecule of the Month:pdb67)
related structures by homologous chain: 1QN4, 1QNA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of a yeast TBP/TATA-box complex., Kim Y, Geiger JH, Hahn S, Sigler PB, Nature 1993 Oct 7;365(6446):512-20. PMID:8413604
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (95 Kb) [Save to disk]
  • Biological Unit Coordinates (1ytb.pdb1.gz) 46 Kb
  • Biological Unit Coordinates (1ytb.pdb2.gz) 46 Kb
  • CSU: Contacts of Structural Units for 1YTB
  • Likely Quarternary Molecular Structure file(s) for 1YTB
  • Retrieve 1YTB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YTB from S2C, [Save to disk]
    • View 1YTB 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 1YTB
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1YTB, from MSDmotif at EBI
  • Genome occurence of 1YTB's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ytba2, region A:156-240 [Jmol] [rasmolscript] [script source]
        - Domain d1ytba1, region A:61-155 [Jmol] [rasmolscript] [script source]
        - Domain d1ytbb2, region B:156-240 [Jmol] [rasmolscript] [script source]
        - Domain d1ytbb1, region B:61-155 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ytb 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: [1ytb_B] [1ytb] [1ytb_D] [1ytb_C] [1ytb_A]
  • SWISS-PROT database: [P13393]
  • Domain organization of [TBP_YEAST] by SWISSPFAM
    • Other resources with information on 1YTB
  • Community annotation for 1YTB 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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