5L5W Hydrolase Hydrolase Inhibitor date May 28, 2016
title Yeast 20s Proteasome With Human Beta5c (1-138) And Human Bet 111; 118-133)
authors M.Groll, E.M.Huber
compound source
Molecule: Proteasome Subunit Alpha Type-2
Chain: A, O
Synonym: Macropain Subunit Y7,Multicatalytic Endopeptidase Subunit Y7,Proteasome Component Y7,Proteinase Ysce Subunit
Ec: 3.4.25.1
 Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Proteasome Subunit Alpha Type-3
Chain: B, P
Synonym: Macropain Subunit Y13,Multicatalytic Endopeptidase Subunit Y13,Proteasome Component Y13,Proteinase Ysce Subuni
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Proteasome Subunit Alpha Type-4
Chain: C, Q
Synonym: Macropain Subunit Pre6,Multicatalytic Endopeptidas Subunit Pre6,Proteasome Component Pre6,Proteinase Ysce Subu
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Proteasome Subunit Alpha Type-5
Chain: D, R
Synonym: Macropain Subunit Pup2,Multicatalytic Endopeptidas Subunit Pup2,Proteasome Component Pup2,Proteinase Ysce Subu
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Proteasome Subunit Alpha Type-6
Chain: E, S
Synonym: Macropain Subunit Pre5,Multicatalytic Endopeptidas Subunit Pre5,Proteasome Component Pre5,Proteinase Ysce Subu
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Probable Proteasome Subunit Alpha Type-7
Chain: F, T
Synonym: Macropain Subunit C1,Multicatalytic Endopeptidase Subunit C1,Proteasome Component C1,Proteinase Ysce Subunit
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Proteasome Subunit Alpha Type-1
Chain: G, U
Synonym: Macropain Subunit C7-Alpha,Multicatalytic Endopept Complex C7,Proteasome Component C7-Alpha,Proteasome Compone Proteinase Ysce Subunit 7,Scl1 Suppressor Protein;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Proteasome Subunit Beta Type-2
Chain: H, V
Synonym: Macropain Subunit Pup1,Multicatalytic Endopeptidas Subunit Pup1,Proteasome Component Pup1,Proteinase Ysce Subu
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Proteasome Subunit Beta Type-3
Chain: I, W
Synonym: Macropain Subunit Pup3,Multicatalytic Endopeptidas Subunit Pup3,Proteasome Component Pup3;
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Proteasome Subunit Beta Type-4
Chain: J, X
Synonym: Macropain Subunit C11,Multicatalytic Endopeptidase Subunit C11,Proteasome Component C11,Proteinase Ysce Subuni
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Proteasome Subunit Beta Type-5,Proteasome Subunit Type-5;
Chain: K, Y
Synonym: Macropain Epsilon Chain,Multicatalytic Endopeptida Epsilon Chain,Proteasome Chain 6,Proteasome Epsilon Chain,P Subunit Mb1,Proteasome Subunit X,Macropain Subunit Pre2, Multicatalytic Endopeptidase Complex Subunit Pre2,Proteasom Component Pre2,Proteinase Ysce Subunit Pre2;
Ec: 3.4.25.1,3.4.25.1
Engineered: Yes
Organism_scientific: Homo Sapiens, Saccharomyces Cerevisiae Atcc 204508 S288c);
Organism_common: Human, Baker'S Yeast
Organism_taxid: 9606, 559292
Gene: Psmb5, Lmpx, Mb1, X, Pre2, Doa3, Prg1, Ypr103w, P8283
Expression_system: Saccharomyces Cerevisiae (Strain Atcc 20 S288c);
Expression_system_taxid: 559292

Molecule: Proteasome Subunit Beta Type-6,Proteasome Subunit Type-1,Proteasome Subunit Beta Type-6,Proteasome Subunit Be Proteasome Subunit Beta Type-6;
Chain: L, Z
Synonym: Multicatalytic Endopeptidase Complex Subunit C5,Pr Component C5,Macropain Subunit C5,Multicatalytic Endopeptid Complex Subunit C5,Proteasome Component C5,Proteasome Gamma Multicatalytic Endopeptidase Complex Subunit C5,Proteasome C5,Macropain Subunit C5,Multicatalytic Endopeptidase Comple C5,Proteasome Component C5,Proteasome Gamma Chain,Multicata Endopeptidase Complex Subunit C5,Proteasome Component C5;
Ec: 3.4.25.1,3.4.25.1,3.4.25.1,3.4.25.1,3.4.25.1
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c), Homo Sapiens, Saccharomyces Cerevisiae;
Organism_common: Baker'S Yeast, Human
Organism_taxid: 559292, 9606
Gene: Pre7, Prs3, Pts1, Ybl041w, Ybl0407, Psmb1, Psc5
Expression_system: Saccharomyces Cerevisiae (Strain Atcc 20 S288c);
Expression_system_taxid: 559292

Molecule: Proteasome Subunit Beta Type-7
Chain: M, a
Synonym: Macropain Subunit Pre4,Multicatalytic Endopeptidas Subunit Pre4,Proteasome Component Pre4,Proteinase Ysce Subu
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Proteasome Subunit Beta Type-1
Chain: N, b
Synonym: Macropain Subunit Pre3,Multicatalytic Endopeptidas Subunit Pre3,Proteasome Component Pre3,Proteinase Ysce Subu
Ec: 3.4.25.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
symmetry Space Group: P 1 21 1
R_factor 0.185 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.070 300.350 145.240 90.00 112.50 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CL, MG 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


    N, b

  • 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


    a, M

  • proteasome core complex, bet...
    • Primary referenceA humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta5i., Huber EM, Heinemeyer W, de Bruin G, Overkleeft HS, Groll M, EMBO J. 2016 Dec 1;35(23):2602-2613. Epub 2016 Oct 27. PMID:27789522
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2028 Kb) [Save to disk]
  • Biological Unit Coordinates (5l5w.pdb1.gz) 2015 Kb
  • LPC: Ligand-Protein Contacts for 5L5W
  • CSU: Contacts of Structural Units for 5L5W
  • Structure Factors (5429 Kb)
  • Retrieve 5L5W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L5W from S2C, [Save to disk]
  • Re-refined 5l5w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5L5W 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 5L5W
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5l5w_O] [5l5w_L] [5l5w] [5l5w_X] [5l5w_Z] [5l5w_T] [5l5w_Q] [5l5w_D] [5l5w_B] [5l5w_V] [5l5w_K] [5l5w_C] [5l5w_H] [5l5w_a] [5l5w_G] [5l5w_Y] [5l5w_N] [5l5w_U] [5l5w_S] [5l5w_R] [5l5w_F] [5l5w_A] [5l5w_b] [5l5w_E] [5l5w_P] [5l5w_W] [5l5w_M] [5l5w_I] [5l5w_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5L5W: [Proteasome_A_N ] by SMART
    • Other resources with information on 5L5W
  • Community annotation for 5L5W at PDBWiki (http://pdbwiki.org)

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