5L5A Hydrolase Hydrolase Inhibitor date May 28, 2016
title Yeast 20s Proteasome With Human Beta5i (1-138; R57t)
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
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pre8, Prs4, Yml092c
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pre9, Prs5, Ygr135w
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pre6, Yol038w
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pup2, Doa5, Ygr253c, G9155
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pre5, Ymr314w, Ym9924.06
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pre10, Prc1, Prs1, Yor362c, O6650
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Scl1, Prc2, Prs2, Ygl011c
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pup1, Yor157c
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pup3, Yer094c
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pre1, Yer012w
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 559292

Molecule: Proteasome Subunit Beta Type-8,Proteasome Subunit Type-5;
Chain: K, Y
Synonym: Low Molecular Mass Protein 7,Macropain Subunit C13 Multicatalytic Endopeptidase Complex Subunit C13,Proteasome C13,Proteasome Subunit Beta-5i,Really Interesting New Gene Protein,Macropain Subunit Pre2,Multicatalytic Endopeptidase Subunit Pre2,Proteasome Component Pre2,Proteinase Ysce Subu
Ec: 3.4.25.1,3.4.25.1
Engineered: Yes

Organism_scientific: Homo Sapiens, Saccharomyces Cerevisiae
Organism_common: Human, Baker'S Yeast
Organism_taxid: 9606, 559292
Gene: Psmb8, Lmp7, Psmb5i, Ring10, Y2, Pre2, Doa3, Prg1, Yp P8283.10;
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 559292

Molecule: Proteasome Subunit Beta Type-6
Chain: L, Z
Synonym: Multicatalytic Endopeptidase Complex Subunit C5,Pr Component C5;
Ec: 3.4.25.1
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pre7, Prs3, Pts1, Ybl041w, Ybl0407
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pre4, Yfr050c
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Pre3, Yjl001w, J1407
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 559292
symmetry Space Group: P 1 21 1
R_factor 0.200 R_Free 0.219
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.140 301.150 145.060 90.00 112.57 90.00
method X-Ray Diffractionresolution 2.40 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


    N, b

  • proteasome core complex, bet...
  • P, B

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


    S, E

  • proteasome core complex, alp...
  • V, H


    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] (2119 Kb) [Save to disk]
  • Biological Unit Coordinates (5l5a.pdb1.gz) 2104 Kb
  • LPC: Ligand-Protein Contacts for 5L5A
  • CSU: Contacts of Structural Units for 5L5A
  • Structure Factors (8732 Kb)
  • Retrieve 5L5A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L5A from S2C, [Save to disk]
  • Re-refined 5l5a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5L5A 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 5L5A
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5l5a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5l5a_Y] [5l5a_V] [5l5a_E] [5l5a_N] [5l5a_T] [5l5a_H] [5l5a_P] [5l5a] [5l5a_K] [5l5a_L] [5l5a_O] [5l5a_X] [5l5a_B] [5l5a_U] [5l5a_F] [5l5a_R] [5l5a_a] [5l5a_W] [5l5a_I] [5l5a_M] [5l5a_J] [5l5a_b] [5l5a_Z] [5l5a_G] [5l5a_Q] [5l5a_C] [5l5a_A] [5l5a_D] [5l5a_S]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5L5A: [Proteasome_A_N ] by SMART
  • Other resources with information on 5L5A
  • Community annotation for 5L5A at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science