5LEY Hydrolase date Jun 30, 2016
title Human 20s Proteasome Complex With Oprozomib At 1.9 Angstrom
authors J.Schrader, F.Henneberg, R.Mata, K.Tittmann, T.R.Schneider, H.Sta G.Bourenkov, A.Chari
compound source
Molecule: Proteasome Subunit Alpha Type-2
Chain: A, O
Synonym: Macropain Subunit C3,Multicatalytic Endopeptidase Subunit C3,Proteasome Component C3;
Ec: 3.4.25.1
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Alpha Type-4
Chain: B, P
Synonym: Macropain Subunit C9,Multicatalytic Endopeptidase Subunit C9,Proteasome Component C9,Proteasome Subunit L;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Alpha Type-7
Chain: C, Q
Synonym: Proteasome Subunit Rc6-1,Proteasome Subunit Xapc7
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Alpha Type-5
Chain: D, R
Synonym: Macropain Zeta Chain,Multicatalytic Endopeptidase Zeta Chain,Proteasome Zeta Chain;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Alpha Type-1
Chain: E, S
Synonym: 30 Kda Prosomal Protein,Pros-30,Macropain Subunit Multicatalytic Endopeptidase Complex Subunit C2,Proteasome C2,Proteasome Nu Chain;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Alpha Type-3
Chain: F, T
Synonym: Macropain Subunit C8,Multicatalytic Endopeptidase Subunit C8,Proteasome Component C8;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Alpha Type-6
Chain: G, U
Synonym: 27 Kda Prosomal Protein,P27k,Macropain Iota Chain, Multicatalytic Endopeptidase Complex Iota Chain,Proteasome Chain;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Beta Type-7
Chain: H, V
Synonym: Macropain Chain Z,Multicatalytic Endopeptidase Com Z,Proteasome Subunit Z;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Beta Type-3
Chain: I, W
Synonym: Proteasome Chain 13,Proteasome Component C10-II,Pr Theta Chain;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Beta Type-2
Chain: J, X
Synonym: Macropain Subunit C7-I,Multicatalytic Endopeptidas Subunit C7-I,Proteasome Component C7-I;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Beta 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;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Beta Type-1
Chain: L, Z
Synonym: Macropain Subunit C5,Multicatalytic Endopeptidase Subunit C5,Proteasome Component C5,Proteasome Gamma Chain;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Beta Type-4
Chain: M, a
Synonym: 26 Kda Prosomal Protein,Pros-26,Macropain Beta Cha Multicatalytic Endopeptidase Complex Beta Chain,Proteasome Chain,Proteasome Chain 3,Hsn3;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Proteasome Subunit Beta Type-6
Chain: N, b
Synonym: Macropain Delta Chain,Multicatalytic Endopeptidase Delta Chain,Proteasome Delta Chain,Proteasome Subunit Y;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Bound Oprozomib
Chain: c, d
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.188 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
113.390 202.650 315.140 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 1PE, 6V1, 6V9, 6VA, CL, K, MG, OAS, YCM enzyme Hydrolase E.C.3.4.25.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, O


D, R


F, T


G, U
  • positive regulation of NF-ka...

    • J, X


    K, Y


    N, V, H, b


    P, B


    Q, C


    S, E


    W, I


    Z, L


    a, M


    Primary referenceThe inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design., Schrader J, Henneberg F, Mata RA, Tittmann K, Schneider TR, Stark H, Bourenkov G, Chari A, Science. 2016 Aug 5;353(6299):594-8. doi: 10.1126/science.aaf8993. PMID:27493187
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2062 Kb) [Save to disk]
  • Biological Unit Coordinates (5ley.pdb1.gz) 2041 Kb
  • LPC: Ligand-Protein Contacts for 5LEY
  • CSU: Contacts of Structural Units for 5LEY
  • Structure Factors (8363 Kb)
  • Retrieve 5LEY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LEY from S2C, [Save to disk]
  • Re-refined 5ley structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5LEY 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 5LEY
  • 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: [5ley_N] [5ley_d] [5ley_S] [5ley_R] [5ley_A] [5ley_J] [5ley_U] [5ley_K] [5ley_L] [5ley_D] [5ley_I] [5ley_Q] [5ley_Y] [5ley_B] [5ley_C] [5ley_P] [5ley_c] [5ley_X] [5ley_F] [5ley_O] [5ley_T] [5ley_V] [5ley_b] [5ley_a] [5ley_Z] [5ley] [5ley_W] [5ley_G] [5ley_E] [5ley_H] [5ley_M]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5LEY: [Proteasome_A_N ] by SMART
    • Other resources with information on 5LEY
  • Community annotation for 5LEY at PDBWiki (http://pdbwiki.org)

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