4V8X Structure of Thermus thermophilus ribosome date
authors Feng, S., Chen, Y., Kamada, K., Wang, H., Tang, K., Wang, M., Gao, Y.G.
compound source
symmetry
R_factor
R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.35
note 4V8X supersedes 4BYB, 4BYC, 4BYD, 4BYE
Gene
Ontology
ChainFunctionProcessComponent
AB, CB


AC, CC


AH, CH


AI, CI


AL, CL


AM, CM


AN, CN


AO, CO


AS, CS


AT, CT


AU, CU


AY, CZ, AZ, CY
  • endoribonuclease activity
  • endoribonuclease activity, p...


  • B0, D0


    B1, D1


    B3, D3


    B4, D4


    B6, D6


    B7, D7


    BC, DC


    BE, DE


    BF, DF


    BN, DN


    BO, DO


    BQ, DQ


    BS, DS


    BT, DT


    BW, DW


    BX, DX


    BY, DY


    CD, AD


    CE, AE


    CF, AF


    CG, AG


    CJ, AJ


    CK, AK


    CP, AP


    CQ, AQ


    CR, AR


    D2, B2


    D5, B5


    D8, B8


    D9, B9


    DD, BD


    DG, BG


    DH, BH


    DI, BI


    DP, BP


    DR, BR


    DU, BU


    DV, BV


    DZ, BZ


    Primary referenceYoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity., Feng S, Chen Y, Kamada K, Wang H, Tang K, Wang M, Gao YG, Nucleic Acids Res. 2013 Aug 14. PMID:23945936
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1217 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 4V8X
  • Structure Factors (6998 Kb)
  • Retrieve 4V8X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V8X from S2C, [Save to disk]
  • View 4V8X 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 4V8X
  • 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: [4v8x_BB] [4v8x_AU] [4v8x_B5] [4v8x_CL] [4v8x_AA] [4v8x_D5] [4v8x_CB] [4v8x_D4] [4v8x_CF] [4v8x_AF] [4v8x_AI] [4v8x_DX] [4v8x_CR] [4v8x_DZ] [4v8x_DJ] [4v8x_D9] [4v8x_CN] [4v8x_BI] [4v8x_AQ] [4v8x_AD] [4v8x_CI] [4v8x_AK] [4v8x_DD] [4v8x_CG] [4v8x_BQ] [4v8x_AO] [4v8x_B4] [4v8x_AN] [4v8x_AZ] [4v8x_DC] [4v8x_D6] [4v8x_BZ] [4v8x_CK] [4v8x_BU] [4v8x_DA] [4v8x] [4v8x_CS] [4v8x_AT] [4v8x_BC] [4v8x_BE] [4v8x_DV] [4v8x_AL] [4v8x_CU] [4v8x_B2] [4v8x_CA] [4v8x_B3] [4v8x_BH] [4v8x_B1] [4v8x_CO] [4v8x_CJ] [4v8x_CY] [4v8x_BW] [4v8x_DT] [4v8x_BN] [4v8x_AJ] [4v8x_CV] [4v8x_BR] [4v8x_DO] [4v8x_AP] [4v8x_D1] [4v8x_AG] [4v8x_CM] [4v8x_DP] [4v8x_D0] [4v8x_AE] [4v8x_B7] [4v8x_CW] [4v8x_DS] [4v8x_AR] [4v8x_AW] [4v8x_BX] [4v8x_DB] [4v8x_CP] [4v8x_DN] [4v8x_BD] [4v8x_AS] [4v8x_B6] [4v8x_AH] [4v8x_DG] [4v8x_DQ] [4v8x_B9] [4v8x_BV] [4v8x_AM] [4v8x_AC] [4v8x_AY] [4v8x_BS] [4v8x_DY] [4v8x_BF] [4v8x_DW] [4v8x_CH] [4v8x_DI] [4v8x_CQ] [4v8x_BG] [4v8x_DH] [4v8x_AX] [4v8x_CD] [4v8x_DF] [4v8x_DR] [4v8x_DE] [4v8x_CX] [4v8x_BY] [4v8x_CC] [4v8x_B0] [4v8x_D7] [4v8x_B8] [4v8x_CT] [4v8x_D8] [4v8x_CZ] [4v8x_CE] [4v8x_BA] [4v8x_DU] [4v8x_AV] [4v8x_BJ] [4v8x_BP] [4v8x_AB] [4v8x_BT] [4v8x_D2] [4v8x_D3] [4v8x_BO]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V8X: [KH] [KOW] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 4V8X
  • Community annotation for 4V8X at PDBWiki (http://pdbwiki.org)

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