4V5B Structure of PDF binding helix in complex with the ribosome date
authors Bingel-Erlenmeyer, R., Kohler, R., Kramer, G., Sandikci, A., Antolic, S., Maier, T., Schaffitzel, C., Wiedmann, B., Bukau, B., Ban, N.
compound source
symmetry
R_factor
R_Free 0.323
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.74
note 4V5B supersedes 2VHM, 2VHN, 2VHO, 2VHP
Gene
Ontology
ChainFunctionProcessComponent
A3, C3


AC, CC


AH, CH


AI, CI


AL, CL


AM, CM


AN, CN


AO, CO


AS, CS


AT, CT


AU, CU


AX, CX


AY, CY


BB, DB


BC, DC


BE, DE


BF, DF


BL, DL


BN, DN


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


  • BQ, DQ


    BS, DS


    BT, DT
  • ornithine decarboxylase inhi...


  • C0, A0


    C1, A1


    C2, A2


    C4, A4


    CD, AD


    CE, AE


    CF, AF


    CG, AG


    CJ, AJ


    CK, AK


    CP, AP


    CQ, AQ
  • translation repressor activi...


  • CR, AR


    CV, AV


    CW, AW


    CZ, AZ


    DD, BD


    DG, BG


    DH, BH


    DI, BI


    DJ, BJ


    DK, BK


    DM, BM


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


  • DR, BR


    DU, BU


    Primary referenceA peptide deformylase-ribosome complex reveals mechanism of nascent chain processing., Bingel-Erlenmeyer R, Kohler R, Kramer G, Sandikci A, Antolic S, Maier T, Schaffitzel C, Wiedmann B, Bukau B, Ban N, Nature. 2008 Mar 6;452(7183):108-11. Epub 2008 Feb 20. PMID:18288106
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1780 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 4V5B
  • Structure Factors (4315 Kb)
  • Retrieve 4V5B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V5B from S2C, [Save to disk]
  • View 4V5B 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 4V5B
  • 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: [4v5b_CB] [4v5b_BS] [4v5b_BE] [4v5b_AW] [4v5b_DO] [4v5b_AJ] [4v5b_CQ] [4v5b_AH] [4v5b_DP] [4v5b_CC] [4v5b_AM] [4v5b_DD] [4v5b_CN] [4v5b_BC] [4v5b_BI] [4v5b] [4v5b_AN] [4v5b_CA] [4v5b_CY] [4v5b_AK] [4v5b_DR] [4v5b_AR] [4v5b_DS] [4v5b_BB] [4v5b_AY] [4v5b_CP] [4v5b_DF] [4v5b_CU] [4v5b_BL] [4v5b_DL] [4v5b_DN] [4v5b_CH] [4v5b_BN] [4v5b_AZ] [4v5b_A0] [4v5b_A2] [4v5b_DG] [4v5b_BO] [4v5b_DC] [4v5b_CF] [4v5b_CO] [4v5b_AG] [4v5b_DT] [4v5b_C4] [4v5b_AO] [4v5b_DJ] [4v5b_CL] [4v5b_AP] [4v5b_AF] [4v5b_AX] [4v5b_CW] [4v5b_BD] [4v5b_AE] [4v5b_DB] [4v5b_AL] [4v5b_DA] [4v5b_CM] [4v5b_AU] [4v5b_AC] [4v5b_BK] [4v5b_BQ] [4v5b_CS] [4v5b_CR] [4v5b_AT] [4v5b_AA] [4v5b_CZ] [4v5b_AD] [4v5b_CE] [4v5b_A5] [4v5b_BT] [4v5b_BF] [4v5b_AB] [4v5b_CX] [4v5b_CD] [4v5b_BM] [4v5b_C3] [4v5b_A4] [4v5b_DQ] [4v5b_CV] [4v5b_CT] [4v5b_C0] [4v5b_AI] [4v5b_A3] [4v5b_A1] [4v5b_AS] [4v5b_CK] [4v5b_BG] [4v5b_DM] [4v5b_AQ] [4v5b_DH] [4v5b_BU] [4v5b_BR] [4v5b_CJ] [4v5b_DU] [4v5b_AV] [4v5b_CG] [4v5b_DE] [4v5b_BA] [4v5b_C1] [4v5b_BH] [4v5b_DI] [4v5b_BP] [4v5b_DK] [4v5b_BJ] [4v5b_CI] [4v5b_C2]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V5B: [KH] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 4V5B
  • Community annotation for 4V5B at PDBWiki (http://pdbwiki.org)

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