4JKR Crystal Structure of E. coli RNA Polymerase in complex with ppGpp date 2013-03-11
authors Zuo, Y., Wang, Y., Steitz, T.A.
compound source
R_Free 0.31802
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 4.20
ligand G4P, SR, ZN enzyme
Gene BWG ; ECDH10B ; ECDH1ME8569 ; ECDH1ME8569 ; ECDH1 ; ECDH1 ; O3K ; O3O ; O3O ; O3O
A, B, H, G

C, I

F, L
  • bacterial sigma factor activ...

  • J, D

    K, E

    Primary referenceThe Mechanism of E. coli RNA Polymerase Regulation by ppGpp Is Suggested by the Structure of their Complex., Zuo Y, Wang Y, Steitz TA, Mol Cell. 2013 May 9;50(3):430-6. doi: 10.1016/j.molcel.2013.03.020. Epub 2013, Apr 25. PMID:23623685
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2613 Kb) [Save to disk]
  • Biological Unit Coordinates (4jkr.pdb1.gz) 1306 Kb
  • Biological Unit Coordinates (4jkr.pdb2.gz) 1309 Kb
  • LPC: Ligand-Protein Contacts for 4JKR
  • CSU: Contacts of Structural Units for 4JKR
  • Structure Factors (1327 Kb)
  • Retrieve 4JKR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JKR from S2C, [Save to disk]
  • Re-refined 4jkr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JKR 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 4JKR
  • 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 4JKR, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jkr_L] [4jkr] [4jkr_E] [4jkr_B] [4jkr_J] [4jkr_G] [4jkr_I] [4jkr_F] [4jkr_K] [4jkr_A] [4jkr_H] [4jkr_C] [4jkr_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4JKR: [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4JKR
  • Community annotation for 4JKR at PDBWiki (http://pdbwiki.org)

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