4YLP E. coli Transcription Initiation Complex - 16-bp spacer and 5-nt RNA date
authors Zuo, Y., Steitz, T.A.
compound source
symmetry
R_factor
R_Free 0.31302
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 5.50
ligand GTP, MG, ZN enzyme
Gene ECE24377A ; ECE24377A ; ECE24377A ; ECE24377A
Gene
Ontology
ChainFunctionProcessComponent
C, O, I


F, L, R
  • bacterial sigma factor activ...


    • J, P, D


    K, E, Q


    N, M, A, B, H, G


    Primary referenceCrystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble., Zuo Y, Steitz TA, Mol Cell. 2015 Apr 8. pii: S1097-2765(15)00175-6. doi:, 10.1016/j.molcel.2015.03.010. PMID:25866247
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (4158 Kb) [Save to disk]
  • Biological Unit Coordinates (4ylp.pdb1.gz) 1397 Kb
  • Biological Unit Coordinates (4ylp.pdb2.gz) 1400 Kb
  • Biological Unit Coordinates (4ylp.pdb3.gz) 1391 Kb
  • LPC: Ligand-Protein Contacts for 4YLP
  • CSU: Contacts of Structural Units for 4YLP
  • Structure Factors (1299 Kb)
  • Retrieve 4YLP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YLP from S2C, [Save to disk]
  • Re-refined 4ylp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4YLP 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 4YLP
  • 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 4YLP, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ylp_L] [4ylp_C] [4ylp_O] [4ylp_D] [4ylp_B] [4ylp_3] [4ylp] [4ylp_N] [4ylp_H] [4ylp_6] [4ylp_8] [4ylp_F] [4ylp_G] [4ylp_R] [4ylp_Q] [4ylp_P] [4ylp_I] [4ylp_1] [4ylp_9] [4ylp_E] [4ylp_4] [4ylp_5] [4ylp_2] [4ylp_J] [4ylp_M] [4ylp_A] [4ylp_K] [4ylp_7]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YLP: [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
    • Other resources with information on 4YLP
  • Community annotation for 4YLP at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science