1YJ1 Structural Protein date Jan 13, 2005
title X-Ray Crystal Structure Of A Chemically Synthesized [D-Gln35
authors D.Bang, G.I.Makhatadze, V.Tereshko, A.A.Kossiakoff, S.B.Kent
compound source
Molecule: Ubiquitin
Chain: A, B, C
Fragment: Residues 1-76
Engineered: Yes
Mutation: Yes
 Synthetic: Yes
Other_details: The Protein Was Chemically Synthesized. The Of The Protein Can Be Naturally Found In Homo Sapiens (Huma
symmetry Space Group: P 21 21 21
R_factor 0.195 R_Free 0.218
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.872 50.395 92.941 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.30 Å
ligand CD, CL, DGN enzyme
related structures by homologous chain: 1OGW
Primary referenceTotal Chemical Synthesis and X-ray Crystal Structure of a Protein Diastereomer: [D-Gln 35]Ubiquitin., Bang D, Makhatadze GI, Tereshko V, Kossiakoff AA, Kent SB, Angew Chem Int Ed Engl 2005 Jun 20;44(25):3852-3856. PMID:15834850
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (1yj1.pdb1.gz) 15 Kb
  • Biological Unit Coordinates (1yj1.pdb2.gz) 15 Kb
  • Biological Unit Coordinates (1yj1.pdb3.gz) 16 Kb
  • Biological Unit Coordinates (1yj1.pdb4.gz) 41 Kb
  • Biological Unit Coordinates (1yj1.pdb5.gz) 41 Kb
  • Biological Unit Coordinates (1yj1.pdb6.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 1YJ1
  • CSU: Contacts of Structural Units for 1YJ1
  • Likely Quarternary Molecular Structure file(s) for 1YJ1
  • Structure Factors (639 Kb)
  • Retrieve 1YJ1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YJ1 from S2C, [Save to disk]
  • Re-refined 1yj1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1YJ1 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 1YJ1
  • 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 1YJ1, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yj1_B] [1yj1_A] [1yj1] [1yj1_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 1YJ1: [UBQ ] by SMART
    • Other resources with information on 1YJ1
  • Community annotation for 1YJ1 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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