4P6F Crystal structure of the peptolide 12C bound to bacterial ribosome date
authors Fagan, C.E., Dunham, C.M.
compound source
symmetry
R_factor
R_Free 0.2542
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.60
note 4P6F supersedes 4W2A, 4W2B, 4W2C, 4W2D
Gene
Ontology
ChainFunctionProcessComponent
QH, XH


QO, XO


QP, XP


QQ, XQ


QR, XR


QT, XT


R0, Y0


R1, Y1


R2, Y2


R3, Y3


R4, Y4


R5, Y5


R8, Y8


R9, Y9


RE, YE


RF, YF


RN, YN


RP, YP


RQ, YQ


RS, YS


RW, YW


RX, YX


XB, QB


XC, QC


XD, QD


XE, QE


XF, QF


XG, QG


XI, QI


XJ, QJ


XK, QK


XL, QL


XM, QM


XN, QN


XS, QS


XU, QU


Y6, R6


Y7, R7


YD, RD


YG, RG


YH, RH


YI, RI


YO, RO


YR, RR


YT, RT


YU, RU


YV, RV


YY, RY


YZ, RZ


Primary referenceMacrolide-Peptide Conjugates as Probes of the Path of Travel of the Nascent Peptides through the Ribosome., Washington AZ, Benicewicz DB, Canzoneri JC, Fagan CE, Mwakwari SC, Maehigashi T, Dunham CM, Oyelere AK, ACS Chem Biol. 2014 Sep 22. PMID:25198768
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2304 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 4P6F
  • Structure Factors (6786 Kb)
  • Retrieve 4P6F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4P6F from S2C, [Save to disk]
  • View 4P6F 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 4P6F
  • 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: [4p6f_R4] [4p6f_Y6] [4p6f_XP] [4p6f_XQ] [4p6f_RI] [4p6f_XG] [4p6f_YB] [4p6f_QJ] [4p6f_XC] [4p6f_YZ] [4p6f_QI] [4p6f_R8] [4p6f_R1] [4p6f_RW] [4p6f_XB] [4p6f_QM] [4p6f_YG] [4p6f_QB] [4p6f_RS] [4p6f_QA] [4p6f_YS] [4p6f_YA] [4p6f_Y1] [4p6f_YF] [4p6f_XW] [4p6f_QH] [4p6f_XJ] [4p6f_XV] [4p6f_YD] [4p6f_R9] [4p6f_RO] [4p6f_XU] [4p6f_QS] [4p6f_R7] [4p6f_RD] [4p6f_XE] [4p6f_R6] [4p6f_RF] [4p6f_R5] [4p6f_RP] [4p6f_XF] [4p6f_Z8] [4p6f_XR] [4p6f_QQ] [4p6f_QT] [4p6f_RE] [4p6f_RG] [4p6f_YQ] [4p6f_QC] [4p6f_XD] [4p6f_Z7] [4p6f_QP] [4p6f_XL] [4p6f_QY] [4p6f_QG] [4p6f_RZ] [4p6f_XO] [4p6f_Y4] [4p6f_YY] [4p6f_R2] [4p6f_Y8] [4p6f_XY] [4p6f_YE] [4p6f_RH] [4p6f_QX] [4p6f_YT] [4p6f_QN] [4p6f_QU] [4p6f_Y5] [4p6f_RR] [4p6f_RV] [4p6f_RQ] [4p6f_RB] [4p6f_YI] [4p6f_QK] [4p6f_R3] [4p6f_QL] [4p6f_XN] [4p6f_QD] [4p6f_YR] [4p6f_QE] [4p6f_YH] [4p6f_QV] [4p6f_Y7] [4p6f_XK] [4p6f_Y3] [4p6f_YV] [4p6f_RT] [4p6f_XI] [4p6f_RA] [4p6f_XH] [4p6f_XA] [4p6f] [4p6f_YO] [4p6f_Y9] [4p6f_RU] [4p6f_YN] [4p6f_QR] [4p6f_QW] [4p6f_YU] [4p6f_YP] [4p6f_QF] [4p6f_Y2] [4p6f_YX] [4p6f_QO] [4p6f_YW] [4p6f_XX] [4p6f_XT] [4p6f_R0] [4p6f_XM] [4p6f_RY] [4p6f_RN] [4p6f_Y0] [4p6f_RX] [4p6f_XS]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4P6F: [KH] [KOW] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 4P6F
  • Community annotation for 4P6F at PDBWiki (http://pdbwiki.org)

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