5LF0 Hydrolase date Jun 30, 2016
title Human 20s Proteasome Complex With Epoxomicin At 2.4 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: Epoxomicin (Peptide Inhibitor)
Chain: c, d, e, f, g, h
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.179 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
113.070 202.370 314.790 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.41 Å
ligand 1PE, 6V1, 6VO, ACE, CL, IML, K, MG, YCM enzyme Hydrolase E.C.3.4.25.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


D, R


F, T


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

  • J, X


    M


    N, K, Y, V, H


    O


    P


    Q, C


    S, E


    W, I


    Z, L


    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] (2135 Kb) [Save to disk]
  • Biological Unit Coordinates (5lf0.pdb1.gz) 2111 Kb
  • LPC: Ligand-Protein Contacts for 5LF0
  • CSU: Contacts of Structural Units for 5LF0
  • Structure Factors (2356 Kb)
  • Retrieve 5LF0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LF0 from S2C, [Save to disk]
  • Re-refined 5lf0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5LF0 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 5LF0
  • 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 5lf0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5lf0_P] [5lf0_E] [5lf0_O] [5lf0_D] [5lf0_X] [5lf0_R] [5lf0_S] [5lf0_G] [5lf0_Y] [5lf0_C] [5lf0_H] [5lf0_e] [5lf0_c] [5lf0_L] [5lf0_W] [5lf0_b] [5lf0_h] [5lf0_N] [5lf0_T] [5lf0_Z] [5lf0_d] [5lf0_B] [5lf0_M] [5lf0_U] [5lf0_I] [5lf0_f] [5lf0_K] [5lf0_F] [5lf0_a] [5lf0_g] [5lf0] [5lf0_A] [5lf0_J] [5lf0_Q] [5lf0_V]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5LF0: [Proteasome_A_N ] by SMART
  • Other resources with information on 5LF0
  • Community annotation for 5LF0 at PDBWiki (http://pdbwiki.org)

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