3BDM Hydrolase date Nov 15, 2007
title Yeast 20s Proteasome:Glidobactin A-Complex
authors M.Groll, R.Dudler, M.Kaiser
compound source
Molecule: Proteasome Component Y7
Chain: A, O
Synonym: Macropain Subunit Y7, Proteinase Ysce Subunit 7, Multicatalytic Endopeptidase Complex Subunit Y7;
Ec: 3.4.25.1
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303

Molecule: Proteasome Component Y13
Chain: B, P
Synonym: Macropain Subunit Y13, Proteinase Ysce Subunit 13, Multicatalytic Endopeptidase Complex Subunit Y13;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303

Molecule: Proteasome Component Pre6
Chain: C, Q
Synonym: Macropain Subunit Pre6, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre6;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303

Molecule: Proteasome Component Pup2
Chain: D, R
Synonym: Macropain Subunit Pup2, Proteinase Ysce Subunit Pu Multicatalytic Endopeptidase Complex Subunit Pup2;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303

Molecule: Proteasome Component Pre5
Chain: E, S
Synonym: Macropain Subunit Pre5, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre5;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303

Molecule: Proteasome Component C1
Chain: F, T
Synonym: Macropain Subunit C1, Proteinase Ysce Subunit 1, Multicatalytic Endopeptidase Complex Subunit C1;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303

Molecule: Proteasome Component C7-Alpha
Chain: G, U
Synonym: Macropain Subunit C7- Alpha, Proteinase Ysce Subun Multicatalytic Endopeptidase Complex C7, Proteasome Compone Scl1 Suppressor Protein;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303

Molecule: Proteasome Component Pup1
Chain: H, V
Synonym: Macropain Subunit Pup1, Proteinase Ysce Subunit Pu Multicatalytic Endopeptidase Complex Subunit Pup1;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303

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: 4932
Strain: W303

Molecule: Proteasome Component C11
Chain: J, X
Synonym: Macropain Subunit C11, Proteinase Ysce Subunit 11, Multicatalytic Endopeptidase Complex Subunit C11;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303

Molecule: Proteasome Component Pre2
Chain: K, Y
Synonym: Macropain Subunit Pre2, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre2;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303

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: 4932
Strain: W303

Molecule: Proteasome Component Pre4
Chain: M, 0
Synonym: Macropain Subunit Pre4, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre4;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303

Molecule: Proteasome Component Pre3
Chain: N, 1
Synonym: Macropain Subunit Pre3, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre3;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: W303
symmetry Space Group: P 1 21 1
R_factor 0.234 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
132.770 302.790 143.210 90.00 112.24 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand GDT enzyme Hydrolase E.C.3.4.25.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, O

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

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

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

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

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


    M, 0

  • proteasome core complex, bet...
    • N, 1

  • 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 referenceA plant pathogen virulence factor inhibits the eukaryotic proteasome by a novel mechanism., Groll M, Schellenberg B, Bachmann AS, Archer CR, Huber R, Powell TK, Lindow S, Kaiser M, Dudler R, Nature. 2008 Apr 10;452(7188):755-8. PMID:18401409
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1019 Kb) [Save to disk]
  • Biological Unit Coordinates (3bdm.pdb1.gz) 1010 Kb
  • LPC: Ligand-Protein Contacts for 3BDM
  • CSU: Contacts of Structural Units for 3BDM
  • Likely Quarternary Molecular Structure file(s) for 3BDM
  • Structure Factors (2263 Kb)
  • Retrieve 3BDM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BDM from S2C, [Save to disk]
  • Re-refined 3bdm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3BDM 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 3BDM
  • 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 3BDM, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bdm_W] [3bdm_P] [3bdm] [3bdm_L] [3bdm_A] [3bdm_B] [3bdm_S] [3bdm_U] [3bdm_J] [3bdm_E] [3bdm_T] [3bdm_0] [3bdm_G] [3bdm_O] [3bdm_C] [3bdm_N] [3bdm_1] [3bdm_D] [3bdm_M] [3bdm_Z] [3bdm_X] [3bdm_K] [3bdm_I] [3bdm_H] [3bdm_R] [3bdm_Y] [3bdm_V] [3bdm_Q] [3bdm_F]
  • SWISS-PROT database: [P40302] [P23639] [P21242] [P23638] [P32379] [P21243] [P40303] [P23724] [P22141] [P25451] [P30657] [P30656] [P38624] [P25043]
  • Domain organization of [PSA1_YEAST] [PSA2_YEAST] [PSA3_YEAST] [PSA4_YEAST] [PSA5_YEAST] [PSA6_YEAST] [PSA7_YEAST] [PSB1_YEAST] [PSB2_YEAST] [PSB3_YEAST] [PSB4_YEAST] [PSB5_YEAST] [PSB6_YEAST] [PSB7_YEAST] by SWISSPFAM
  • Domain found in 3BDM: [Proteasome_A_N ] by SMART
    • Other resources with information on 3BDM
  • Community annotation for 3BDM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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  • Images from IMB Jena Image Library of Biological Macromolecules.

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