3TDD Hydrolase Hydrolase Inhibitor date Aug 10, 2011
title Crystal Structure Of Yeast Cp In Complex With Belactosin C
authors V.S.Korotkov, A.Ludwig, O.V.Larionov, A.V.Lygin, M.Groll, A.De Me
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 0.212 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.930 301.600 144.200 90.00 112.94 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand BFO 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 referenceSynthesis and biological activity of optimized belactosin C congeners., Korotkov VS, Ludwig A, Larionov OV, Lygin AV, Groll M, de Meijere A, Org Biomol Chem. 2011 Sep 23. PMID:21946808
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1014 Kb) [Save to disk]
  • Biological Unit Coordinates (3tdd.pdb1.gz) 1007 Kb
  • LPC: Ligand-Protein Contacts for 3TDD
  • CSU: Contacts of Structural Units for 3TDD
  • Structure Factors (2392 Kb)
  • Retrieve 3TDD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3TDD from S2C, [Save to disk]
  • Re-refined 3tdd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3TDD 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 3TDD
  • 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 3TDD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3tdd_C] [3tdd_J] [3tdd_H] [3tdd_G] [3tdd_W] [3tdd_Y] [3tdd_M] [3tdd_A] [3tdd_Z] [3tdd_T] [3tdd_1] [3tdd_D] [3tdd_O] [3tdd_F] [3tdd_E] [3tdd_S] [3tdd_Q] [3tdd_K] [3tdd] [3tdd_B] [3tdd_U] [3tdd_I] [3tdd_2] [3tdd_N] [3tdd_P] [3tdd_V] [3tdd_L] [3tdd_X] [3tdd_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3TDD: [Proteasome_A_N ] by SMART
    • Other resources with information on 3TDD
  • Community annotation for 3TDD at PDBWiki (http://pdbwiki.org)
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  • Images from IMB Jena Image Library of Biological Macromolecules.

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