4V57 Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin and neomycin. date
authors Borovinskaya, M.A., Shoji, S., Holton, J.M., Fredrick, K., Cate, J.H.D.
compound source
symmetry
R_factor
R_Free 0.306
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.50
note 4V57 supersedes 2QOY, 2QOZ, 2QP0, 2QP1
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 4V57
  • Structure Factors (4952 Kb)
  • Retrieve 4V57 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V57 from S2C, [Save to disk]
    • View 4V57 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 4V57
  • 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: [4v57_DB] [4v57_DX] [4v57_CL] [4v57_DT] [4v57_CP] [4v57_AS] [4v57_BR] [4v57_AB] [4v57_AA] [4v57_DM] [4v57_CJ] [4v57_AJ] [4v57_DO] [4v57_BB] [4v57_BM] [4v57_AR] [4v57_AD] [4v57_DY] [4v57_BU] [4v57_B3] [4v57_AL] [4v57_CU] [4v57_AQ] [4v57_AM] [4v57_BZ] [4v57_BS] [4v57_AK] [4v57_DZ] [4v57_DP] [4v57_BA] [4v57_BE] [4v57_BF] [4v57_BQ] [4v57_CN] [4v57_D4] [4v57_AH] [4v57_CK] [4v57_CC] [4v57_DU] [4v57_DJ] [4v57_AN] [4v57_CA] [4v57_BP] [4v57_BN] [4v57_AF] [4v57_DI] [4v57_CT] [4v57_BD] [4v57_DF] [4v57_BI] [4v57_AE] [4v57_DV] [4v57_B4] [4v57_BV] [4v57_DQ] [4v57_DR] [4v57_D3] [4v57_DN] [4v57_CE] [4v57_BH] [4v57_B1] [4v57_BX] [4v57_B2] [4v57_DG] [4v57_CR] [4v57_DC] [4v57_CS] [4v57_D0] [4v57_DS] [4v57_BJ] [4v57_CH] [4v57_BT] [4v57_DA] [4v57_DE] [4v57_DD] [4v57] [4v57_CD] [4v57_AO] [4v57_CB] [4v57_CQ] [4v57_AI] [4v57_BC] [4v57_AP] [4v57_AU] [4v57_D1] [4v57_D2] [4v57_B0] [4v57_BY] [4v57_BL] [4v57_DL] [4v57_AT] [4v57_BO] [4v57_BW] [4v57_AC] [4v57_AG] [4v57_BG] [4v57_CG] [4v57_DW] [4v57_CO] [4v57_DK] [4v57_BK] [4v57_CF] [4v57_CM] [4v57_CI] [4v57_DH]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V57: [KH] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 4V57
  • Community annotation for 4V57 at PDBWiki (http://pdbwiki.org)

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