2O5J Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analog date
authors Vassylyev, D.G., Vassylyeva, M.N.
compound source
R_Free 0.257
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.00
ligand APC, MG, ZN enzyme
A, K, B, L

M, C

N, D

O, E

Primary referenceStructural basis for substrate loading in bacterial RNA polymerase., Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R, Nature. 2007 Jun 20;. PMID:17581591
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1047 Kb) [Save to disk]
  • Biological Unit Coordinates (2o5j.pdb1.gz) 525 Kb
  • Biological Unit Coordinates (2o5j.pdb2.gz) 524 Kb
  • LPC: Ligand-Protein Contacts for 2O5J
  • CSU: Contacts of Structural Units for 2O5J
  • Likely Quarternary Molecular Structure file(s) for 2O5J
  • Structure Factors (2169 Kb)
  • Retrieve 2O5J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2O5J from S2C, [Save to disk]
  • Re-refined 2o5j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2O5J 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 2O5J
  • 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 2O5J, from MSDmotif at EBI
  • Fold representative 2o5j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2o5j_Y] [2o5j_O] [2o5j_D] [2o5j_H] [2o5j_E] [2o5j_G] [2o5j_B] [2o5j_C] [2o5j_A] [2o5j_M] [2o5j_N] [2o5j_Z] [2o5j_I] [2o5j] [2o5j_L] [2o5j_X] [2o5j_K]
  • SWISS-PROT database: [Q5SHR6] [Q8RQE9] [Q8RQE8] [Q8RQE7]
  • Domain organization of [RPOA_THET8] [RPOB_THET8] [RPOC_THET8] [RPOZ_THET8] by SWISSPFAM
  • Domains found in 2O5J: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 2O5J
  • Community annotation for 2O5J 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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