4UD7 Structure of the stapled peptide YS-02 bound to MDM2 date
authors Tan, Y.S., Reeks, J., Brown, C.J., Jennings, C.E., Eapen, R.S., Tng, Q.S., Thean, D., Ying, Y.T., Gago, F.J.F., Lane, D.P., Noble, M.E.M., Verma, C.
compound source
symmetry
R_factor
R_Free 0.17838
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.60
ligand 2JN, ACE, NH2 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceBenzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design., Tan YS, Reeks J, Brown CJ, Thean D, Ferrer Gago FJ, Yuen TY, Goh ET, Lee XE, Jennings CE, Joseph TL, Lakshminarayanan R, Lane DP, Noble ME, Verma CS, J Phys Chem Lett. 2016 Sep 1;7(17):3452-7. doi: 10.1021/acs.jpclett.6b01525. Epub, 2016 Aug 22. PMID:27532490
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (168 Kb) [Save to disk]
  • Biological Unit Coordinates (4ud7.pdb1.gz) 41 Kb
  • Biological Unit Coordinates (4ud7.pdb2.gz) 40 Kb
  • Biological Unit Coordinates (4ud7.pdb3.gz) 42 Kb
  • Biological Unit Coordinates (4ud7.pdb4.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 4UD7
  • CSU: Contacts of Structural Units for 4UD7
  • Structure Factors (653 Kb)
  • Retrieve 4UD7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UD7 from S2C, [Save to disk]
  • Re-refined 4ud7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4UD7 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 4UD7
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ud7_H] [4ud7_G] [4ud7_I] [4ud7_A] [4ud7_F] [4ud7_B] [4ud7] [4ud7_C] [4ud7_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4UD7
  • Community annotation for 4UD7 at PDBWiki (http://pdbwiki.org)

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