2F16

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.231 
  • R-Value Observed: 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
  • Structures With Same Primary Citation

  • 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, München, Germany. mgroll@med.uni-muenchen.de



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome component Y7
A, O
250Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23639

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome component Y13
B, P
244Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23638

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE6
C, Q
241Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP2
D, R
242Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE5
E, S
233Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C1
F, T
244Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C7-alpha
G, U
243Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP1
H, V
222Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP3
I, W
204Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C11
J, X
198Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE2
K, Y
212Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C5
L, Z
222Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE4
1, M
233Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE3
2, N
196Saccharomyces cerevisiaeMutation(s): 0 
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 CCD File 
2, H, K, N, V, Y
N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
C19 H25 B N4 O4
GXJABQQUPOEUTA-RDJZCZTQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.175α = 90
b = 300.716β = 113.28
c = 144.659γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance