6HV5 Hydrolase date Oct 10, 2018
title Yeast 20s Proteasome With Human Beta2i (1-53) In Complex Wit
authors E.M.Huber, M.Groll
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-10,Proteasome Subuni Type-2;
Chain: H, V
Synonym: Low Molecular Mass Protein 10,Macropain Subunit Me Multicatalytic Endopeptidase Complex Subunit Mecl-1,Proteas 1,Proteasome Subunit Beta-2i,Macropain Subunit Pup1,Multica Endopeptidase Complex Subunit Pup1,Proteasome Component Pup Proteinase Ysce Subunit Pup1;
Ec: 3.4.25.1,3.4.25.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens, Saccharomyces Cerevisiae Atcc 204508 S288c);
Organism_common: Human, Baker'S Yeast
Organism_taxid: 9606, 559292
Gene: Psmb10, Lmp10, Mecl1, Pup1, Yor157c
Expression_system: Saccharomyces Cerevisiae S288c
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
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
Chain: K, Y
Synonym: Macropain Subunit Pre2,Multicatalytic Endopeptidas Subunit Pre2,Proteasome Component Pre2,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-6
Chain: L, Z
Synonym: Multicatalytic Endopeptidase Complex Subunit C5,Pr Component C5;
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-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 0.173 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.690 300.440 144.130 90.00 112.59 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand CL, GQH, 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 referenceStructure-based design of inhibitors selective for human proteasome beta2c or beta2i subunits., Xin BT, Huber E, de Bruin G, Heinemeyer W, Maurits E, Espinal C, Du Y, Janssens M, Weyburne ES, Kisselev A, Florea BI, Driessen C, van der Marel GA, Groll M, Overkleeft HS, J Med Chem. 2019 Jan 18. doi: 10.1021/acs.jmedchem.8b01884. PMID:30657666
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2072 Kb) [Save to disk]
  • Biological Unit Coordinates (6hv5.pdb1.gz) 2058 Kb
  • LPC: Ligand-Protein Contacts for 6HV5
  • CSU: Contacts of Structural Units for 6HV5
  • Structure Factors (5938 Kb)
  • Retrieve 6HV5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6HV5 from S2C, [Save to disk]
    • View 6HV5 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 6HV5
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6hv5_N] [6hv5_B] [6hv5_D] [6hv5_T] [6hv5_V] [6hv5_I] [6hv5_G] [6hv5_P] [6hv5_C] [6hv5_M] [6hv5_Z] [6hv5_H] [6hv5_K] [6hv5_F] [6hv5_S] [6hv5_E] [6hv5_J] [6hv5_a] [6hv5_Y] [6hv5_R] [6hv5_W] [6hv5_A] [6hv5_L] [6hv5_b] [6hv5_X] [6hv5_O] [6hv5_Q] [6hv5_U]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6HV5
  • Community annotation for 6HV5 at PDBWiki (http://pdbwiki.org)

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