4V56 Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin. date
authors Borovinskaya, M.A., Shoji, S., Holton, J.M., Fredrick, K., Cate, J.H.D.
compound source
symmetry
R_factor
R_Free 0.311
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.93
note 4V56 supersedes 2QOU, 2QOV, 2QOW, 2QOX
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 referenceA steric block in translation caused by the antibiotic spectinomycin., Borovinskaya MA, Shoji S, Holton JM, Fredrick K, Cate JH, ACS Chem Biol. 2007 Aug 17;2(8):545-52. Epub 2007 Aug 10. PMID:17696316
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (959 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 4V56
  • Structure Factors (3748 Kb)
  • Retrieve 4V56 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V56 from S2C, [Save to disk]
  • View 4V56 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 4V56
  • 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: [4v56_DH] [4v56_B2] [4v56_DK] [4v56_AC] [4v56_AJ] [4v56_BT] [4v56_BU] [4v56_DA] [4v56_BG] [4v56_B4] [4v56_DN] [4v56_CK] [4v56_CS] [4v56_BZ] [4v56_CI] [4v56_DG] [4v56_CT] [4v56_CR] [4v56_BR] [4v56_AB] [4v56_CB] [4v56_BO] [4v56_DS] [4v56_D4] [4v56_CC] [4v56_AI] [4v56_CN] [4v56_BI] [4v56_DE] [4v56_CF] [4v56_AG] [4v56_CL] [4v56_BW] [4v56_BX] [4v56_BY] [4v56_CD] [4v56_CM] [4v56_AD] [4v56_B1] [4v56_CJ] [4v56_DO] [4v56_DX] [4v56_DD] [4v56_AN] [4v56_CP] [4v56_AP] [4v56_BK] [4v56_DR] [4v56_DL] [4v56_DY] [4v56_AR] [4v56_AT] [4v56_BC] [4v56_DP] [4v56_CU] [4v56_AA] [4v56_BP] [4v56_DB] [4v56_AS] [4v56_CO] [4v56_CQ] [4v56_AU] [4v56_DZ] [4v56_BD] [4v56_CA] [4v56_AM] [4v56_BN] [4v56_DM] [4v56_AF] [4v56_DU] [4v56_D0] [4v56_D2] [4v56_DQ] [4v56_AQ] [4v56_DT] [4v56_BQ] [4v56_CH] [4v56_DI] [4v56_BV] [4v56_D1] [4v56_CE] [4v56_AO] [4v56_BS] [4v56_AL] [4v56_DV] [4v56] [4v56_BL] [4v56_D3] [4v56_BM] [4v56_DF] [4v56_BF] [4v56_BE] [4v56_B3] [4v56_B0] [4v56_AK] [4v56_DJ] [4v56_DW] [4v56_AH] [4v56_DC] [4v56_BB] [4v56_CG] [4v56_AE] [4v56_BH] [4v56_BA] [4v56_BJ]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V56: [KH] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 4V56
  • Community annotation for 4V56 at PDBWiki (http://pdbwiki.org)

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