4EU2 Hydrolase Hydrolase Inhibitor date Apr 25, 2012
title Crystal Structure Of 20s Proteasome With Novel Inhibitor K-7
authors J.Kikuchi, N.Shibayama, S.Yamada, T.Wada, M.Nobuyoshi, T.Izumi, M. Y.Kano, M.Ohki, K.Sugiyama, S.Y.Park, Y.Furukawa
compound source
Molecule: Proteasome Component C7-Alpha
Chain: A, O
Fragment: Unp Residues 10-250
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: S288c

Molecule: Proteasome Component Y7
Chain: B, P
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: S288c

Molecule: Proteasome Component Y13
Chain: C, Q
Fragment: Unp Residues 2-245
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: S288c

Molecule: Proteasome Component Pre6
Chain: D, R
Fragment: Unp Residues 3-243
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: S288c

Molecule: Proteasome Component Pup2
Chain: E, S
Fragment: Unp Residues 9-250
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: S288c

Molecule: Proteasome Component Pre5
Chain: F, T
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: S288c

Molecule: Proteasome Component C1
Chain: G, U
Fragment: Unp Residues 5-248
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: S288c

Molecule: Proteasome Component Pre3
Chain: H, V
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: S288c

Molecule: Proteasome Component Pup1
Chain: I, W
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: S288c

Molecule: Proteasome Component Pup3
Chain: J, X
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: S288c

Molecule: Proteasome Component C11
Chain: K, Y
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: S288c

Molecule: Proteasome Component Pre2
Chain: L, Z
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: S288c

Molecule: Proteasome Component C5
Chain: M, 1
Synonym: Multicatalytic Endopeptidase Complex Subunit C5
Ec: 3.4.25.1

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: S288c

Molecule: Proteasome Component Pre4
Chain: N, 2
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: S288c
symmetry Space Group: P 1 21 1
R_factor 0.202 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.264 301.363 143.964 90.00 112.86 90.00
method X-Ray Diffractionresolution 2.51 Å
ligand WPI enzyme Hydrolase E.C.3.4.25.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
1, M

  • proteasome core complex, bet...
  • A, O

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


    F, T

  • proteasome core complex, alp...
  • G, U


    J, X
  • endopeptidase activator acti...

  • proteasome core complex, bet...
  • K, Y
  • endopeptidase activator acti...

  • proteasome core complex, bet...
  • N, 2


    P, B

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

  • proteasome core complex, alp...
  • S, E

  • proteasome core complex, alp...
  • V, H

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


    Primary referenceHomopiperazine derivatives as a novel class of proteasome inhibitors with a unique mode of proteasome binding., Kikuchi J, Shibayama N, Yamada S, Wada T, Nobuyoshi M, Izumi T, Akutsu M, Kano Y, Sugiyama K, Ohki M, Park SY, Furukawa Y, PLoS One. 2013 Apr 11;8(4):e60649. doi: 10.1371/journal.pone.0060649. Print 2013. PMID:23593271
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1029 Kb) [Save to disk]
  • Biological Unit Coordinates (4eu2.pdb1.gz) 1020 Kb
  • LPC: Ligand-Protein Contacts for 4EU2
  • CSU: Contacts of Structural Units for 4EU2
  • Structure Factors (4971 Kb)
  • Retrieve 4EU2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4EU2 from S2C, [Save to disk]
  • Re-refined 4eu2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4EU2 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 4EU2
  • 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 4EU2, from MSDmotif at EBI
  • Fold representative 4eu2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4eu2_K] [4eu2_T] [4eu2_X] [4eu2_1] [4eu2_A] [4eu2_S] [4eu2_R] [4eu2_Y] [4eu2_H] [4eu2_E] [4eu2_N] [4eu2_C] [4eu2_F] [4eu2_G] [4eu2_I] [4eu2_B] [4eu2_Q] [4eu2_U] [4eu2_W] [4eu2] [4eu2_P] [4eu2_L] [4eu2_V] [4eu2_M] [4eu2_O] [4eu2_D] [4eu2_2] [4eu2_Z] [4eu2_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4EU2: [Proteasome_A_N ] by SMART
  • Other resources with information on 4EU2
  • Community annotation for 4EU2 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science