3SDI Structure of yeast 20S open-gate proteasome with Compound 20 date
authors Sintchak, M.D.
compound source
R_Free 0.2532
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.65
ligand 3SD, MES, MG enzyme
1, M

A, O

  • proteasome core complex, alp...
  • D, R

  • proteasome core complex, alp...
  • F, T

    G, U

  • proteasome core complex, alp...
  • J, X
  • endopeptidase activator acti...

  • proteasome core complex, bet...
  • K, Y, V, H

    N, 2

  • proteasome core complex, bet...
  • P, B

  • proteasome core complex, alp...
  • Q, C

    S, E

  • proteasome core complex, alp...
  • W, I
  • endopeptidase activator acti...

  • proteasome core complex, bet...
  • Z, L

    Primary referenceOptimization of a series of dipeptides with a P3 threonine residue as non-covalent inhibitors of the chymotrypsin-like activity of the human 20S proteasome., Blackburn C, Barrett C, Blank JL, Bruzzese FJ, Bump N, Dick LR, Fleming P, Garcia K, Hales P, Hu Z, Jones M, Liu JX, Sappal DS, Sintchak MD, Tsu C, Gigstad KM, Bioorg Med Chem Lett. 2010 Nov 15;20(22):6581-6. Epub 2010 Sep 15. PMID:20875739
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (992 Kb) [Save to disk]
  • Biological Unit Coordinates (3sdi.pdb1.gz) 982 Kb
  • LPC: Ligand-Protein Contacts for 3SDI
  • CSU: Contacts of Structural Units for 3SDI
  • Structure Factors (4844 Kb)
  • Retrieve 3SDI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SDI from S2C, [Save to disk]
  • Re-refined 3sdi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SDI 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 3SDI
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3SDI, from MSDmotif at EBI
  • Fold representative 3sdi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3sdi_N] [3sdi_S] [3sdi_T] [3sdi_V] [3sdi_D] [3sdi_Y] [3sdi_U] [3sdi_Z] [3sdi_P] [3sdi_E] [3sdi_Q] [3sdi_H] [3sdi_M] [3sdi_W] [3sdi_J] [3sdi] [3sdi_C] [3sdi_G] [3sdi_I] [3sdi_L] [3sdi_R] [3sdi_O] [3sdi_X] [3sdi_B] [3sdi_F] [3sdi_K] [3sdi_1] [3sdi_2] [3sdi_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3SDI: [Proteasome_A_N ] by SMART
  • Other resources with information on 3SDI
  • Community annotation for 3SDI at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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