5L5H Hydrolase Hydrolase Inhibitor date May 28, 2016
title Yeast 20s Proteasome With Human Beta5i (1-138) And Human Bet 111; 118-133) In Complex With Pr-924
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 (Strain Atcc 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 (Strain Atcc 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 (Strain Atcc 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 (Strain Atcc 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 (Strain Atcc 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 (Strain Atcc 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 (Strain Atcc 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 (Strain Atcc 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 (Strain Atcc 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 (Strain Atcc 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 Atcc 204508 S288c);
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,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 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 (Strain Atcc 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 (Strain Atcc 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 0.194 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.070 300.220 145.500 90.00 112.87 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand 39V, CL, MES, 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] (2101 Kb) [Save to disk]
  • Biological Unit Coordinates (5l5h.pdb1.gz) 2085 Kb
  • LPC: Ligand-Protein Contacts for 5L5H
  • CSU: Contacts of Structural Units for 5L5H
  • Structure Factors (6639 Kb)
  • Retrieve 5L5H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L5H from S2C, [Save to disk]
  • Re-refined 5l5h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5L5H 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 5L5H
  • 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 5l5h from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5l5h_O] [5l5h_Q] [5l5h_H] [5l5h_Z] [5l5h] [5l5h_C] [5l5h_A] [5l5h_D] [5l5h_B] [5l5h_X] [5l5h_L] [5l5h_U] [5l5h_a] [5l5h_N] [5l5h_T] [5l5h_E] [5l5h_P] [5l5h_V] [5l5h_I] [5l5h_Y] [5l5h_b] [5l5h_K] [5l5h_F] [5l5h_G] [5l5h_J] [5l5h_S] [5l5h_M] [5l5h_W] [5l5h_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5L5H: [Proteasome_A_N ] by SMART
  • Other resources with information on 5L5H
  • Community annotation for 5L5H at PDBWiki (http://pdbwiki.org)

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