4R67 Hydrolase Hydrolase Inhibitor date Aug 22, 2014
title Human Constitutive 20s Proteasome In Complex With Carfilzomi
authors J.C.Sacchettini, W.H.Harshbarger
compound source
Molecule: Proteasome Subunit Alpha Type-6
Chain: A, O, c, q
Synonym: 27 Kda Prosomal Protein, Pros-27, P27k, Macropain Chain, Multicatalytic Endopeptidase Complex Iota Chain, Pro Iota Chain;
Ec: 3.4.25.1
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Red Blood Cells

Molecule: Proteasome Subunit Alpha Type-2
Chain: B, P, d, r
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: Red Blood Cells

Molecule: Proteasome Subunit Alpha Type-4
Chain: C, Q, e, s
Fragment: Unp Residues 2-251
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: Red Blood Cells

Molecule: Proteasome Subunit Alpha Type-7
Chain: D, R, f, t
Fragment: Unp Residues 2-244
Synonym: Proteasome Subunit Rc6-1, Proteasome Subunit Xapc7
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Red Blood Cells

Molecule: Proteasome Subunit Alpha Type-5
Chain: E, S, g, u
Fragment: Unp Residues 8-241
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: Red Blood Cells

Molecule: Proteasome Subunit Alpha Type-1
Chain: F, T, h, v
Fragment: Unp Residues 4-241
Synonym: 30 Kda Prosomal Protein, Pros-30, Macropain Subuni 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: Red Blood Cells

Molecule: Proteasome Subunit Alpha Type-3
Chain: G, U, I, w
Fragment: Unp Residues 2-246
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: Red Blood Cells

Molecule: Proteasome Subunit Beta Type-6
Chain: H, V, j, x
Fragment: Unp Residues 35-236
Synonym: Macropain Delta Chain, Multicatalytic Endopeptidas Delta Chain, Proteasome Delta Chain, Proteasome Subunit Y;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Red Blood Cells

Molecule: Proteasome Subunit Beta Type-7
Chain: I, W, k, y
Fragment: Unp Residues 44-263
Synonym: Macropain Chain Z, Multicatalytic Endopeptidase Co Chain Z, Proteasome Subunit Z;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Red Blood Cells

Molecule: Proteasome Subunit Beta Type-3
Chain: J, X, l, z
Synonym: Proteasome Chain 13, Proteasome Component C10-II, Theta Chain;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Red Blood Cells

Molecule: Proteasome Subunit Beta Type-2
Chain: K, Y, m, 0
Fragment: Unp Residues 1-199
Synonym: Macropain Subunit C7-I, Multicatalytic Endopeptida Subunit C7-I, Proteasome Component C7-I;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Red Blood Cells

Molecule: Proteasome Subunit Beta Type-5
Chain: L, Z, n, 3
Fragment: Unp Residues 60-260
Synonym: Macropain Epsilon Chain, Multicatalytic Endopeptid Complex Epsilon Chain, Proteasome Chain 6, Proteasome Epsil Proteasome Subunit Mb1, Proteasome Subunit X;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Red Blood Cells

Molecule: Proteasome Subunit Beta Type-1
Chain: M, 1, o, a
Fragment: Unp Residues 29-241
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: Red Blood Cells

Molecule: Proteasome Subunit Beta Type-4
Chain: N, 2, p, b
Fragment: Unp Residues 46-262
Synonym: 26 Kda Prosomal Protein, Hsbpros26, Pros-26, Macro Chain, Multicatalytic Endopeptidase Complex Beta Chain, Pro Beta Chain, Proteasome Chain 3, Hsn3;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Red Blood Cells
symmetry Space Group: P 1 21 1
R_factor 0.215 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
171.989 201.027 225.585 90.00 107.93 90.00
method X-Ray Diffractionresolution 2.89 Å
ligand 3BV enzyme Hydrolase E.C.3.4.25.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
G, U, w, i


J, z, X, l


K, Y, 0, m


N, 2, b, p


S, E, u, g


T, v, F, h


Z, L, n, 3


a, 1, M, o


c, q, A, O
  • positive regulation of NF-ka...

    • d, B, r, P


    e, s, Q, C


    j, y, k, W, H, I, x, V


    t, D, f, R


    Primary referenceCrystal Structure of the Human 20S Proteasome in Complex with Carfilzomib., Harshbarger W, Miller C, Diedrich C, Sacchettini J, Structure. 2015 Feb 3;23(2):418-24. doi: 10.1016/j.str.2014.11.017. Epub 2015 Jan, 15. PMID:25599644
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1971 Kb) [Save to disk]
  • Biological Unit Coordinates (4r67.pdb1.gz) 993 Kb
  • Biological Unit Coordinates (4r67.pdb2.gz) 990 Kb
  • LPC: Ligand-Protein Contacts for 4R67
  • CSU: Contacts of Structural Units for 4R67
  • Structure Factors (5277 Kb)
  • Retrieve 4R67 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4R67 from S2C, [Save to disk]
  • Re-refined 4r67 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4R67 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 4R67
  • 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
  • 3D motif for 4R67, from MSDmotif at EBI
  • Fold representative 4r67 from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4r67_O] [4r67_S] [4r67_W] [4r67_y] [4r67_l] [4r67_t] [4r67_h] [4r67_Z] [4r67_P] [4r67_U] [4r67_C] [4r67_Q] [4r67_f] [4r67_M] [4r67_d] [4r67_o] [4r67_J] [4r67_p] [4r67_K] [4r67] [4r67_E] [4r67_N] [4r67_1] [4r67_u] [4r67_R] [4r67_L] [4r67_F] [4r67_r] [4r67_I] [4r67_a] [4r67_j] [4r67_q] [4r67_X] [4r67_2] [4r67_n] [4r67_V] [4r67_D] [4r67_T] [4r67_k] [4r67_H] [4r67_c] [4r67_G] [4r67_b] [4r67_i] [4r67_e] [4r67_B] [4r67_s] [4r67_v] [4r67_0] [4r67_A] [4r67_x] [4r67_m] [4r67_z] [4r67_Y] [4r67_3] [4r67_w] [4r67_g]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4R67: [Proteasome_A_N ] by SMART
    • Other resources with information on 4R67
  • Community annotation for 4R67 at PDBWiki (http://pdbwiki.org)

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