1JD2 Hydrolase Hydrolase Inhibitor date Jun 12, 2001
title Crystal Structure Of The Yeast 20s Proteasome:Tmc-95a Comple Covalent Proteasome Inhibitor
authors M.Groll, Y.Koguchi, R.Huber, J.Kohno
compound source
Molecule: Proteasome Component Y7
Chain: A, V
Synonym: Macropain Subunit Y7, Proteinase Ysce Subunit 7, Multicatalytic Endopeptidase Complex Subunit Y7;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component Y13
Chain: B, W
Synonym: Macropain Subunit Y13, Proteinase Ysce Subunit 13, Multicatalytic Endopeptidase Complex Subunit Y13;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component Pre6
Chain: C, X
Synonym: Macropain Subunit Pre6, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre6;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component Pup2
Chain: D, Y
Synonym: Macropain Subunit Pup2, Proteinase Ysce Subunit Pu Multicatalytic Endopeptidase Complex Subunit Pup2;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component Pre5
Chain: E, Z
Synonym: Macropain Subunit Pre5, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre5;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component C1
Chain: F, 1
Synonym: Macropain Subunit C1, Proteinase Ysce Subunit 1, Multicatalytic Endopeptidase Complex Subunit C1;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component C7-Alpha
Chain: G, 2
Synonym: Macropain Subunit C7-Alpha, Proteinase Ysce Subuni Multicatalytic Endopeptidase Complex C7, Component Y8, Scl1 Suppressor Protein;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component Pup1
Chain: H, O
Synonym: Macropain Subunit Pup1, Proteinase Ysce Subunit Pu Multicatalytic Endopeptidase Complex Subunit Pup1;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component Pup3
Chain: I, P
Synonym: Macropain Subunit Pup3, Multicatalytic Endopeptida Subunit Pup3;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component C11
Chain: J, Q
Synonym: Macropain Subunit C11, Proteinase Ysce Subunit 11, Multicatalytic Endopeptidase Complex Subunit C11;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component Pre2
Chain: K, R
Synonym: Macropain Subunit Pre2, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre2;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component C5
Chain: L, S
Synonym: Multicatalytic Endopeptidase Complex Subunit C5
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component Pre4
Chain: M, T
Synonym: Macropain Subunit Pre4, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre4;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Proteasome Component Pre3
Chain: N, U
Synonym: Macropain Subunit Pre3, Proteinase Ysce Subunit Pr Multicatalytic Endopeptidase Complex Subunit Pre3;
Ec: 3.4.99.46
Other_details: Part Of 20s Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Variant: Sub61

Molecule: Tmc-95a Inhibitor
Chain: 8, 9
Organism_scientific: Apiospora Montagnei
Organism_taxid: 255776
symmetry Space Group: P 1 21 1
R_factor 0.251 R_Free 0.336
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.200 301.300 144.800 90.00 112.60 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand 1QQ, AKK, MG, R4K enzyme Hydrolase E.C.3.4.99.46 BRENDA
related structures by homologous chain: 1G0U, 1IRU
Gene
Ontology
ChainFunctionProcessComponent
2, G

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


    E, Z

  • proteasome core complex, alp...
    • F, 1


    K, O, H, R


    N, U

  • proteasome core complex, bet...
    • P, I
  • endopeptidase activator acti...

  • proteasome core complex, bet...
    • Q, J
  • endopeptidase activator acti...

  • proteasome core complex, bet...
    • S, L


    T, M


    V, A

  • proteasome core complex, alp...
    • W, B

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


    Primary referenceCrystal structure of the 20 S proteasome:TMC-95A complex: a non-covalent proteasome inhibitor., Groll M, Koguchi Y, Huber R, Kohno J, J Mol Biol 2001 Aug 17;311(3):543-8. PMID:11493007
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1070 Kb) [Save to disk]
  • Biological Unit Coordinates (1jd2.pdb1.gz) 1062 Kb
  • LPC: Ligand-Protein Contacts for 1JD2
  • CSU: Contacts of Structural Units for 1JD2
  • Likely Quarternary Molecular Structure file(s) for 1JD2
  • Retrieve 1JD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JD2 from S2C, [Save to disk]
    • View 1JD2 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 1JD2
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1JD2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jd21_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1jd22_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1jd2a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1jd2b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1jd2c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1jd2d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1jd2e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1jd2f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1jd2g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1jd2h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1jd2i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1jd2j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1jd2k_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1jd2l_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1jd2m_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1jd2n_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1jd2o_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1jd2p_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1jd2q_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1jd2r_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1jd2s_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1jd2t_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1jd2u_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1jd2v_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1jd2w_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1jd2x_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1jd2y_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1jd2z_, region Z [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1jd2_1] [1jd2_R] [1jd2_A] [1jd2_8] [1jd2_O] [1jd2] [1jd2_X] [1jd2_9] [1jd2_U] [1jd2_N] [1jd2_B] [1jd2_D] [1jd2_Q] [1jd2_W] [1jd2_Y] [1jd2_P] [1jd2_I] [1jd2_F] [1jd2_Z] [1jd2_C] [1jd2_K] [1jd2_H] [1jd2_S] [1jd2_E] [1jd2_2] [1jd2_V] [1jd2_M] [1jd2_J] [1jd2_T] [1jd2_G] [1jd2_L]
  • 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 1JD2: [Proteasome_A_N ] by SMART
    • Other resources with information on 1JD2
  • Community annotation for 1JD2 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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