2BE5 Transferase date Oct 22, 2005
title Crystal Structure Of The T. Thermophilus Rna Polymerase Holo Complex With Inhibitor Tagetitoxin
authors D.G.Vassylyev, V.Svetlov, M.N.Vassylyeva, A.Perederina, N.Igaras N.Matsugaki, S.Wakatsuki, I.Artsimovitch, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Dna-Directed Rna Polymerase Alpha Chain
Chain: A, B, K, L
Synonym: Rnap Alpha Subunit, Transcriptase Alpha Chain, Rna Polymerase Alpha Subunit;
Ec: 2.7.7.6
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Dna-Directed Rna Polymerase Beta Chain
Chain: C, M
Synonym: Rnap Beta Subunit, Transcriptase Beta Chain, Rna P Beta Subunit;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Dna-Directed Rna Polymerase Beta' Chain
Chain: D, N
Synonym: Rnap Beta' Subunit, Transcriptase Beta' Chain, Rna Polymerase Beta' Subunit;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Rna Polymerase Omega Chain
Chain: E, O
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Rna Polymerase Sigma Factor Rpod
Chain: F, P
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 32
R_factor 0.237 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
239.500 239.500 253.100 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand MG, TGT, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, K, B, L


F, P
  • bacterial sigma factor activ...


    • M, C


    N, D


    O, E


    Primary referenceStructural basis for transcription inhibition by tagetitoxin., Vassylyev DG, Svetlov V, Vassylyeva MN, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Artsimovitch I, Nat Struct Mol Biol 2005 Dec;12(12):1086-1093. Epub 2005 Nov 6. PMID:16273103
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1234 Kb) [Save to disk]
  • Biological Unit Coordinates (2be5.pdb1.gz) 624 Kb
  • Biological Unit Coordinates (2be5.pdb2.gz) 615 Kb
  • LPC: Ligand-Protein Contacts for 2BE5
  • CSU: Contacts of Structural Units for 2BE5
  • Likely Quarternary Molecular Structure file(s) for 2BE5
  • Structure Factors (4574 Kb)
  • Retrieve 2BE5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BE5 from S2C, [Save to disk]
  • Re-refined 2be5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2BE5 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 2BE5
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2BE5, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2be5_F] [2be5_B] [2be5_O] [2be5_M] [2be5_C] [2be5_N] [2be5_P] [2be5_E] [2be5_D] [2be5_A] [2be5] [2be5_L] [2be5_K]
  • SWISS-PROT database: [Q5SKW1] [Q5SHR6] [Q9Z9H6] [Q8RQE9] [Q8RQE8] [Q8RQE7]
  • Domain organization of [Q5SKW1_THET8] [RPOA_THET8] [RPOA_THETH] [RPOB_THET8] [RPOC_THET8] [RPOZ_THET8] by SWISSPFAM
  • Domains found in 2BE5: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
    • Other resources with information on 2BE5
  • Community annotation for 2BE5 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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