4V9D Structures of the bacterial ribosome in classical and hybrid states of tRNA binding date
authors Dunkle, J.A., Wang, L., Feldman, M.B., Pulk, A., Chen, V.B., Kapral, G.J., Noeske, J., Richardson, J.S., Blanchard, S.C., Cate, J.H.D.
compound source
symmetry
R_factor
R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.00
note 4V9D supersedes 3R8S, 3R8T, 4GD1, 4GD2, 3R8N, 3R8O
Gene
Ontology
ChainFunctionProcessComponent
AC, BC


AD, BD


AG, BG


AH, BH


AJ, BJ


AK, BK


AM, BM


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


  • AR, BR


    AT, BT
  • ornithine decarboxylase inhi...


  • AU, BU


    AY


    BB, AB


    BE, AE


    BF, AF


    BI, AI


    BL, AL


    BN, AN


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


  • BQ, AQ


    BS, AS


    C0, D0


    C1, D1


    C2, D2


    C4, D4


    CD, DD


    CE, DE


    CF, DF


    CL, DL


    CM, DM


    CN, DN


    CO, DO


    CQ, DQ
  • translation repressor activi...


  • CR, DR


    CT, DT


    CV, DV


    CW, DW


    CX, DX


    CZ, DZ


    D3, C3


    DC, CC


    DG, CG


    DH, CH


    DI, CI


    DJ, CJ


    DK, CK


    DP, CP


    DS, CS


    DU, CU


    DY, CY


    Primary referenceStructures of the bacterial ribosome in classical and hybrid states of tRNA binding., Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JH, Science. 2011 May 20;332(6032):981-4. PMID:21596992
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1759 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 4V9D
  • Structure Factors (10203 Kb)
  • Retrieve 4V9D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V9D from S2C, [Save to disk]
  • View 4V9D 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 4V9D
  • 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: [4v9d_D4] [4v9d_BQ] [4v9d_CS] [4v9d_AE] [4v9d_DD] [4v9d_CO] [4v9d_CX] [4v9d_C1] [4v9d_AA] [4v9d_CA] [4v9d_CV] [4v9d_BN] [4v9d_CW] [4v9d_BC] [4v9d_BI] [4v9d_AS] [4v9d_BV] [4v9d_DT] [4v9d_DS] [4v9d_DM] [4v9d_DC] [4v9d_DG] [4v9d_BR] [4v9d_AG] [4v9d_DI] [4v9d_AV] [4v9d_BK] [4v9d_CI] [4v9d_CU] [4v9d_CQ] [4v9d_CL] [4v9d_AN] [4v9d_AB] [4v9d_BL] [4v9d_AX] [4v9d_AU] [4v9d_CR] [4v9d_DW] [4v9d_C0] [4v9d_BM] [4v9d_DE] [4v9d_D0] [4v9d_CE] [4v9d_AY] [4v9d_AH] [4v9d_DV] [4v9d_CH] [4v9d_BG] [4v9d_C4] [4v9d_CP] [4v9d_AO] [4v9d_DL] [4v9d_DN] [4v9d_AC] [4v9d_DB] [4v9d_BU] [4v9d_CY] [4v9d_AP] [4v9d_C2] [4v9d_CG] [4v9d_DJ] [4v9d_BX] [4v9d_DF] [4v9d_CB] [4v9d] [4v9d_CM] [4v9d_AD] [4v9d_DA] [4v9d_DX] [4v9d_D3] [4v9d_BH] [4v9d_BS] [4v9d_CT] [4v9d_CK] [4v9d_DR] [4v9d_C3] [4v9d_BT] [4v9d_BA] [4v9d_AK] [4v9d_DO] [4v9d_AJ] [4v9d_BE] [4v9d_CD] [4v9d_DH] [4v9d_AI] [4v9d_BD] [4v9d_BO] [4v9d_BP] [4v9d_CZ] [4v9d_DY] [4v9d_DU] [4v9d_D1] [4v9d_BB] [4v9d_AF] [4v9d_AT] [4v9d_AR] [4v9d_D2] [4v9d_AQ] [4v9d_CF] [4v9d_BF] [4v9d_DK] [4v9d_DP] [4v9d_CJ] [4v9d_AM] [4v9d_BJ] [4v9d_AL] [4v9d_DZ] [4v9d_DQ] [4v9d_CN] [4v9d_CC]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V9D: [KH] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 4V9D
  • Community annotation for 4V9D at PDBWiki (http://pdbwiki.org)

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