3OEV Hydrolase Hydrolase Inhibitor date Aug 13, 2010
title Structure Of Yeast 20s Open-Gate Proteasome With Compound 25
authors M.D.Sintchak
compound source
Molecule: Proteasome Component Y7
Chain: A, O
Synonym: Macropain Subunit Y7, Multicatalytic Endopeptidase Subunit Y7, Proteinase Ysce Subunit 7;
Ec: 3.4.25.1
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component Y13
Chain: B, P
Synonym: Macropain Subunit Y13, Multicatalytic Endopeptidas Subunit Y13, Proteinase Ysce Subunit 13;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component Pre6
Chain: C, Q
Synonym: Macropain Subunit Pre6, Multicatalytic Endopeptida Subunit Pre6, Proteinase Ysce Subunit Pre6;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component Pup2
Chain: D, R
Synonym: Macropain Subunit Pup2, Multicatalytic Endopeptida Subunit Pup2, Proteinase Ysce Subunit Pup2;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component Pre5
Chain: E, S
Synonym: Macropain Subunit Pre5, Multicatalytic Endopeptida Subunit Pre5, Proteinase Ysce Subunit Pre5;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component C1
Chain: F, T
Synonym: Macropain Subunit C1, Multicatalytic Endopeptidase Subunit C1, Proteinase Ysce Subunit 1;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component C7-Alpha
Chain: G, U
Synonym: Macropain Subunit C7-Alpha, Multicatalytic Endopep Complex C7, Proteasome Component Y8, Proteinase Ysce Subuni Suppressor Protein;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component Pup1
Chain: H, V
Synonym: Macropain Subunit Pup1, Multicatalytic Endopeptida Subunit Pup1, Proteinase Ysce Subunit Pup1;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component Pup3
Chain: I, W
Synonym: Macropain Subunit Pup3, Multicatalytic Endopeptida Subunit Pup3;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component C11
Chain: J, X
Synonym: Macropain Subunit C11, Multicatalytic Endopeptidas Subunit C11, Proteinase Ysce Subunit 11;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component Pre2
Chain: K, Y
Synonym: Macropain Subunit Pre2, Multicatalytic Endopeptida Subunit Pre2, Proteinase Ysce Subunit Pre2;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component C5
Chain: L, Z
Synonym: Multicatalytic Endopeptidase Complex Subunit C5
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component Pre4
Chain: M, 1
Synonym: Macropain Subunit Pre4, Multicatalytic Endopeptida Subunit Pre4, Proteinase Ysce Subunit Pre4;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome Component Pre3
Chain: N, 2
Synonym: Macropain Subunit Pre3, Multicatalytic Endopeptida Subunit Pre3, Proteinase Ysce Subunit Pre3;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
symmetry Space Group: P 1 21 1
R_factor 0.220 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
136.067 299.946 145.621 90.00 113.17 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand 3OE, MES, MG enzyme Hydrolase E.C.3.4.25.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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] (981 Kb) [Save to disk]
  • Biological Unit Coordinates (3oev.pdb1.gz) 972 Kb
  • LPC: Ligand-Protein Contacts for 3OEV
  • CSU: Contacts of Structural Units for 3OEV
  • Structure Factors (4040 Kb)
  • Retrieve 3OEV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OEV from S2C, [Save to disk]
  • Re-refined 3oev structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3OEV 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 3OEV
  • 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 3OEV, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3oev_N] [3oev_C] [3oev_O] [3oev_V] [3oev_R] [3oev_U] [3oev_Z] [3oev_F] [3oev_M] [3oev_T] [3oev_B] [3oev_I] [3oev_J] [3oev_X] [3oev_K] [3oev_Q] [3oev_L] [3oev_G] [3oev] [3oev_1] [3oev_W] [3oev_Y] [3oev_D] [3oev_A] [3oev_2] [3oev_P] [3oev_H] [3oev_S] [3oev_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3OEV: [Proteasome_A_N ] by SMART
    • Other resources with information on 3OEV
  • Community annotation for 3OEV at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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