4JYA Crystal structures of pseudouridinilated stop codons with ASLs date
authors Fernandez, I.S., Ng, C.L., Kelley, A.C., Guowei, W., Yu, Y.T., Ramakrishnan, V.
compound source
symmetry
R_factor
R_Free 0.2318
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.10
ligand MG, PAR, PSU enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


Primary referenceUnusual base pairing during the decoding of a stop codon by the ribosome., Fernandez IS, Ng CL, Kelley AC, Wu G, Yu YT, Ramakrishnan V, Nature. 2013 Jun 30. doi: 10.1038/nature12302. PMID:23812587
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1048 Kb) [Save to disk]
  • Biological Unit Coordinates (4jya.pdb1.gz) 1040 Kb
  • LPC: Ligand-Protein Contacts for 4JYA
  • CSU: Contacts of Structural Units for 4JYA
  • Structure Factors (4143 Kb)
  • Retrieve 4JYA in mmCIF format [Save to disk]
  • Re-refined 4jya structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4JYA 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 4JYA
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4JYA, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jya] [4jya_M] [4jya_O] [4jya_I] [4jya_A] [4jya_U] [4jya_S] [4jya_C] [4jya_E] [4jya_B] [4jya_N] [4jya_K] [4jya_H] [4jya_P] [4jya_D] [4jya_L] [4jya_G] [4jya_R] [4jya_Y] [4jya_J] [4jya_Q] [4jya_X] [4jya_F] [4jya_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4JYA: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 4JYA
  • Community annotation for 4JYA at PDBWiki (http://pdbwiki.org)

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