3GPT Hydrolase date Mar 23, 2009
title Crystal Structure Of The Yeast 20s Proteasome In Complex Wit Salinosporamide Derivatives: Slow Substrate Ligand
authors M.Groll, V.R.Macherla, R.R.Manam, K.A.M.Arthur, C.B.Potts
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: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component Y13
Chain: B, P
Fragment: Sequence Database Residues 2-245
Synonym: Macropain Subunit Y13, Proteinase Ysce Subunit 13, Multicatalytic Endopeptidase Complex Subunit Y13;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component Pre6
Chain: C, Q
Fragment: Sequence Database Residues 3-243
Synonym: Macropain Subunit Pre6, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre6;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component Pup2
Chain: D, R
Fragment: Sequence Database Residues 9-250
Synonym: Macropain Subunit Pup2, Proteinase Ysce Subunit Pu Multicatalytic Endopeptidase Complex Subunit Pup2;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component Pre5
Chain: E, S
Fragment: Sequence Database Residues 2-234
Synonym: Macropain Subunit Pre5, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre5;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component C1
Chain: F, T
Fragment: Sequence Database Residues 5-248
Synonym: Macropain Subunit C1, Proteinase Ysce Subunit 1, Multicatalytic Endopeptidase Complex Subunit C1;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component C7-Alpha
Chain: G, U
Fragment: Sequence Database Residues 10-252
Synonym: Macropain Subunit C7-Alpha, Proteinase Ysce Subuni Multicatalytic Endopeptidase Complex C7, Proteasome Compone Scl1 Suppressor Protein;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component Pup1
Chain: H, V
Fragment: Sequence Database Residues 30-251
Synonym: Macropain Subunit Pup1, Proteinase Ysce Subunit Pu Multicatalytic Endopeptidase Complex Subunit Pup1;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component Pup3
Chain: I, W
Fragment: Sequence Database Residues 2-205
Synonym: Macropain Subunit Pup3, Multicatalytic Endopeptida Subunit Pup3;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component C11
Chain: J, X
Fragment: Sequence Database Residues 1-198
Synonym: Macropain Subunit C11, Proteinase Ysce Subunit 11, Multicatalytic Endopeptidase Complex Subunit C11;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component Pre2
Chain: K, Y
Fragment: Sequence Database Residues 76-287
Synonym: Macropain Subunit Pre2, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre2;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component C5
Chain: L, Z
Fragment: Sequence Database Residues 20-241
Synonym: Multicatalytic Endopeptidase Complex Subunit C5
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component Pre4
Chain: M, 1
Fragment: Sequence Database Residues 34-266
Synonym: Macropain Subunit Pre4, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre4;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Proteasome Component Pre3
Chain: N, 2
Fragment: Sequence Database Residues 20-215
Synonym: Macropain Subunit Pre3, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre3;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
symmetry Space Group: P 1 21 1
R_factor 0.226 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.000 301.260 143.810 90.00 112.56 90.00
method X-Ray Diffractionresolution 2.41 Å
ligand GPT 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 referenceSnapshots of the fluorosalinosporamide/20S complex offer mechanistic insights for fine tuning proteasome inhibition., Groll M, McArthur KA, Macherla VR, Manam RR, Potts BC, J Med Chem. 2009 Sep 10;52(17):5420-8. PMID:19678642
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1015 Kb) [Save to disk]
  • Biological Unit Coordinates (3gpt.pdb1.gz) 1009 Kb
  • LPC: Ligand-Protein Contacts for 3GPT
  • CSU: Contacts of Structural Units for 3GPT
  • Structure Factors (3250 Kb)
  • Retrieve 3GPT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GPT from S2C, [Save to disk]
  • Re-refined 3gpt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3GPT 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 3GPT
  • 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 3GPT, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gpt_I] [3gpt_U] [3gpt_V] [3gpt_C] [3gpt_2] [3gpt_S] [3gpt_B] [3gpt_E] [3gpt_Y] [3gpt_J] [3gpt_A] [3gpt_P] [3gpt_N] [3gpt] [3gpt_H] [3gpt_G] [3gpt_Q] [3gpt_D] [3gpt_F] [3gpt_L] [3gpt_M] [3gpt_R] [3gpt_T] [3gpt_1] [3gpt_X] [3gpt_O] [3gpt_W] [3gpt_K] [3gpt_Z]
  • 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 3GPT: [Proteasome_A_N ] by SMART
    • Other resources with information on 3GPT
  • Community annotation for 3GPT at PDBWiki (http://pdbwiki.org)
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