1VY6 Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site. date
authors Polikanov, Y.S., Steitz, T.A., Innis, C.A.
compound source
symmetry
R_factor
R_Free 0.2862
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.90
note 1VY6 supersedes 4QCU, 4QCV, 4QCW, 4QCX
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


B0, D0


B1, D1


B3, D3


B4, D4


B6, D6


B7, D7


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 referenceA proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome., Polikanov YS, Steitz TA, Innis CA, Nat Struct Mol Biol. 2014 Aug 17. doi: 10.1038/nsmb.2871. PMID:25132179
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1049 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1VY6
  • Structure Factors (14040 Kb)
  • Retrieve 1VY6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VY6 from S2C, [Save to disk]
  • View 1VY6 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 1VY6
  • 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: [1vy6_DO] [1vy6_CO] [1vy6_D0] [1vy6_BA] [1vy6_AI] [1vy6_AM] [1vy6_AK] [1vy6_B8] [1vy6_CW] [1vy6_BT] [1vy6_AW] [1vy6_D8] [1vy6_D7] [1vy6_AR] [1vy6_AU] [1vy6_D9] [1vy6_DD] [1vy6_CE] [1vy6_BD] [1vy6_D2] [1vy6_BO] [1vy6_AV] [1vy6_DN] [1vy6_BB] [1vy6_DQ] [1vy6_AJ] [1vy6_AA] [1vy6_CI] [1vy6_DV] [1vy6_AH] [1vy6_DR] [1vy6_CN] [1vy6_B2] [1vy6_B7] [1vy6_DH] [1vy6_CD] [1vy6_DB] [1vy6_BX] [1vy6_BS] [1vy6_CA] [1vy6_CV] [1vy6_CL] [1vy6_D4] [1vy6_D5] [1vy6_DT] [1vy6_CQ] [1vy6_AT] [1vy6_AD] [1vy6_AP] [1vy6_BG] [1vy6_CB] [1vy6_DA] [1vy6_B9] [1vy6_AC] [1vy6_AS] [1vy6_DU] [1vy6_B6] [1vy6_BI] [1vy6_BZ] [1vy6_CT] [1vy6_B3] [1vy6_BV] [1vy6_AE] [1vy6_CP] [1vy6_BU] [1vy6_AG] [1vy6_AX] [1vy6_BY] [1vy6_BQ] [1vy6_AB] [1vy6_DX] [1vy6_B5] [1vy6_AQ] [1vy6_CK] [1vy6_B1] [1vy6_BN] [1vy6_CJ] [1vy6] [1vy6_CR] [1vy6_CX] [1vy6_CG] [1vy6_DP] [1vy6_DI] [1vy6_CS] [1vy6_DE] [1vy6_BE] [1vy6_AF] [1vy6_B0] [1vy6_DY] [1vy6_D1] [1vy6_CF] [1vy6_AL] [1vy6_CM] [1vy6_AN] [1vy6_CU] [1vy6_BF] [1vy6_DS] [1vy6_B4] [1vy6_CC] [1vy6_BW] [1vy6_DZ] [1vy6_DW] [1vy6_D6] [1vy6_AO] [1vy6_BH] [1vy6_BR] [1vy6_CH] [1vy6_D3] [1vy6_DG] [1vy6_DF] [1vy6_BP]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 1VY6: [KH] [KOW] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 1VY6
  • Community annotation for 1VY6 at PDBWiki (http://pdbwiki.org)

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