2F16

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.

(2006) Structure 14: 451-456

  • DOI: 10.1016/j.str.2005.11.019

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Department for Physiological Chemistry, Ludwig-Maximilians-University, Butenandtstrasse 5, Building B 81377, M√ľnchen, Germany. mgroll@med.uni-muenchen.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome component Y7
A, O
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE8 (PRS4)
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23639
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome component Y13
B, P
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE9 (PRS5)
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23638
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE6
C, Q
241Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE6
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP2
D, R
242Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PUP2 (DOA5)
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32379
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE5
E, S
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE5
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40302
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C1
F, T
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE10 (PRC1, PRS1)
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21242
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C7-alpha
G, U
243Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SCL1 (PRC2, PRS2)
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21243
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP1
H, V
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PUP1
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25043
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP3
I, W
204Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PUP3
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25451
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C11
J, X
198Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE1
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22141
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE2
K, Y
212Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE2 (DOA3, PRG1)
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30656
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C5
L, Z
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE7 (PRS3, PTS1)
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23724
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE4
M, 1
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE4
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30657
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE3
N, 2
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE3
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BO2
Query on BO2

Download SDF File 
Download CCD File 
2, H, K, N, V, Y
N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
BORTEZOMIB
C19 H25 B N4 O4
GXJABQQUPOEUTA-RDJZCZTQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 136.175α = 90.00
b = 300.716β = 113.28
c = 144.659γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-11-14 
  • Released Date: 2006-03-21 
  • Deposition Author(s): Groll, M.

Revision History 

  • Version 1.0: 2006-03-21
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance