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
  • Primary Citation of Related Structures:  
    2F16

  • 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 yeast 20S proteasome in complex with bortezomib to establish the specificity and binding mode of bortezomib to the proteasome's different catalytically active sites ...

    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 LengthOrganismDetailsImage
Proteasome component Y7A, O250Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component Y13B, P244Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE6C, Q241Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP2D, R242Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE5E, S233Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C1F, T244Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 7
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Proteasome component C7-alphaG, U243Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP1H, V222Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 9
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Proteasome component PUP3I, W204Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 10
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Proteasome component C11J, X198Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 11
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Proteasome component PRE2K, Y212Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C5L, Z222Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 13
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Proteasome component PRE4AA [auth 1], M233Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE3BA [auth 2], N196Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BO2
Query on BO2

Download Ideal Coordinates CCD File 
CA [auth H], DA [auth K], EA [auth N], FA [auth V], GA [auth Y], HA [auth 2]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  (Full details and data files)

  • 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