ISDA

Deposition Date 2005-11-14

Release Date 2006-03-21

Last Version Date 2024-10-30

Entry Detail

PDB ID:

2F16

Keywords:

HYDROLASE

Title:

Crystal structure of the yeast 20S proteasome in complex with bortezomib

Biological Source:

Source Organism:

Saccharomyces cerevisiae (Taxon ID: 4932)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.80 Å

R-Value Free:

0.26

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 1 21 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component Y7
Gene (Uniprot):PRE8
Chain IDs:A, O
Chain Length:250
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P23639 Pfam ID:PF10584, PF00227

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component Y13
Gene (Uniprot):PRE9
Chain IDs:B, P
Chain Length:244
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P23638 Pfam ID:PF10584, PF00227

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE6
Gene (Uniprot):PRE6
Chain IDs:C, Q
Chain Length:241
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P40303 Pfam ID:PF10584, PF00227

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP2
Gene (Uniprot):PUP2
Chain IDs:D, R
Chain Length:242
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P32379 Pfam ID:PF10584, PF00227

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE5
Gene (Uniprot):PRE5
Chain IDs:E, S
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P40302 Pfam ID:PF10584, PF00227

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component C1
Gene (Uniprot):PRE10
Chain IDs:F, T
Chain Length:244
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P21242 Pfam ID:PF10584, PF00227

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component C7-alpha
Gene (Uniprot):SCL1
Chain IDs:G, U
Chain Length:243
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P21243 Pfam ID:PF10584, PF00227 EC:3.4.25.1

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP1
Gene (Uniprot):PUP1
Chain IDs:H, V
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P25043 Pfam ID:PF00227, PF12465

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP3
Gene (Uniprot):PUP3
Chain IDs:I, W
Chain Length:204
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P25451 Pfam ID:PF00227

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component C11
Gene (Uniprot):PRE1
Chain IDs:J, X
Chain Length:198
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P22141 Pfam ID:PF00227

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE2
Gene (Uniprot):PRE2
Chain IDs:K, Y
Chain Length:212
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P30656 Pfam ID:PF00227

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component C5
Gene (Uniprot):PRE7
Chain IDs:L, Z
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P23724 Pfam ID:PF00227

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE4
Gene (Uniprot):PRE4
Chain IDs:M, AA (auth: 1)
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P30657 Pfam ID:PF00227

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE3
Gene (Uniprot):PRE3
Chain IDs:N, BA (auth: 2)
Chain Length:196
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38624 Pfam ID:PF00227 EC:3.4.25.1

Ligand Molecules

BO2

Primary Citation

Crystal Structure of the Boronic Acid-Based Proteasome Inhibitor Bortezomib in Complex with the Yeast 20S Proteasome.

Groll, M, Berkers, C.R, Ploegh, H.L, Ovaa, H.Show

Structure 14 451 456 (2006)

PMID: 16531229 DOI: 10.1016/j.str.2005.11.019

Abstact

The dipeptide boronic acid bortezomib, also termed VELCADE, is a proteasome inhibitor now in use for the treatment of multiple myeloma, and its use for the treatment of other malignancies is being explored. We determined the crystal structure of the yeast 20S proteasome in complex with bortezomib to establish the specificity and binding mode of bortezomib to the proteasome's different catalytically active sites. This structure should enable the rational design of new boronic acid derivatives with improved affinities and specificities for individual active subunits.

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Primary Citation of related structures