4V64 Crystal structure of the bacterial ribosome from Escherichia coli in complex with hygromycin B. date
authors Borovinskaya, M.A., Shoji, S., Fredrick, K., Cate, J.H.D.
compound source
symmetry
R_factor
R_Free 0.318
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.50
note 4V64 supersedes 3DF1, 3DF2, 3DF3, 3DF4
Gene
Ontology
ChainFunctionProcessComponent
AB, CB


AC, CC


AH, CH


AI, CI


AL, CL


AM, CM


AN, CN


AO, CO
  • mRNA binding involved in pos...


    • AS, CS


    AT, CT
  • ornithine decarboxylase inhi...


    • AU, CU


    B0, D0


    B1, D1


    B3, D3


    B4, D4


    BC, DC


    BE, DE


    BF, DF


    BL, DL


    BN, DN


    BO, DO


    BQ, DQ
  • translation repressor activi...


    • BS, DS


    BT, DT


    BW, DW


    BX, DX


    BY, DY


    CD, AD


    CE, AE


    CF, AF


    CG, AG


    CJ, AJ


    CK, AK


    CP, AP
  • nuclease activity
  • endonuclease activity
  • endodeoxyribonuclease activi...


    • CQ, AQ


    CR, AR


    D2, B2


    DD, BD


    DG, BG


    DH, BH


    DI, BI


    DJ, BJ


    DK, BK


    DM, BM


    DP, BP


    DR, BR


    DU, BU


    DV, BV


    DZ, BZ


    Primary referenceStructural basis for hygromycin B inhibition of protein biosynthesis., Borovinskaya MA, Shoji S, Fredrick K, Cate JH, RNA. 2008 Aug;14(8):1590-9. Epub 2008 Jun 20. PMID:18567815
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (959 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 4V64
  • Structure Factors (4351 Kb)
  • Retrieve 4V64 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V64 from S2C, [Save to disk]
    • View 4V64 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 4V64
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4v64_CG] [4v64_BU] [4v64_B2] [4v64_AI] [4v64_DD] [4v64_DN] [4v64_DZ] [4v64_DE] [4v64_BF] [4v64_BS] [4v64_CD] [4v64_BE] [4v64_DW] [4v64_AM] [4v64_DM] [4v64_BG] [4v64_CL] [4v64_CE] [4v64_CI] [4v64_DX] [4v64] [4v64_BP] [4v64_AD] [4v64_DG] [4v64_BM] [4v64_BK] [4v64_D2] [4v64_AL] [4v64_CT] [4v64_BI] [4v64_BC] [4v64_CA] [4v64_DB] [4v64_BZ] [4v64_CS] [4v64_B1] [4v64_CC] [4v64_D1] [4v64_BW] [4v64_AO] [4v64_AS] [4v64_BO] [4v64_BY] [4v64_AK] [4v64_BN] [4v64_BQ] [4v64_BA] [4v64_DF] [4v64_BR] [4v64_BB] [4v64_DP] [4v64_DK] [4v64_CR] [4v64_B0] [4v64_B3] [4v64_AA] [4v64_DO] [4v64_BL] [4v64_DJ] [4v64_CP] [4v64_AR] [4v64_D3] [4v64_BJ] [4v64_CU] [4v64_BD] [4v64_BH] [4v64_DL] [4v64_AG] [4v64_CQ] [4v64_AC] [4v64_AJ] [4v64_DT] [4v64_CO] [4v64_AP] [4v64_DU] [4v64_BX] [4v64_AF] [4v64_DV] [4v64_CK] [4v64_CJ] [4v64_AQ] [4v64_DQ] [4v64_CM] [4v64_AT] [4v64_DI] [4v64_BV] [4v64_AN] [4v64_DR] [4v64_DC] [4v64_BT] [4v64_DH] [4v64_AU] [4v64_CN] [4v64_D0] [4v64_DA] [4v64_CF] [4v64_CH] [4v64_D4] [4v64_AH] [4v64_AB] [4v64_DS] [4v64_CB] [4v64_B4] [4v64_DY] [4v64_AE]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V64: [KH] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 4V64
  • Community annotation for 4V64 at PDBWiki (http://pdbwiki.org)

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