3NZJ

Crystal structure of yeast 20S proteasome in complex with ligand 2a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

20S proteasome inhibition: designing noncovalent linear peptide mimics of the natural product TMC-95A.

Groll, M.Gallastegui, N.Marechal, X.Le Ravalec, V.Basse, N.Richy, N.Genin, E.Huber, R.Moroder, L.Vidal, J.Reboud-Ravaux, M.

(2010) ChemMedChem 5: 1701-1705


Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component Y7A, O250Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component Y13B, P258Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE6C, Q254Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP2D, R260Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE5E, S234Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C1F, T288Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C7-alphaG, U252Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP1H, V261Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP3I, W205Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C11J, X198Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE2K, Y287Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C5L, Z241Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE4AA [auth 1],
M
266Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE3BA [auth 2],
N
215Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
TMC-95A mimic ligand 2aCA [auth 3],
DA [auth 4]
5N/AMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
EA [auth K],
FA [auth Y]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
TRO
Query on TRO
CA [auth 3],
DA [auth 4]
L-PEPTIDE LINKINGC11 H12 N2 O3TRP
TY5
Query on TY5
CA [auth 3],
DA [auth 4]
L-PEPTIDE LINKINGC16 H17 N O3TYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 15
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001103
Query on PRD_001103
CA [auth 3], DA [auth 4]TMC-95A mimic ligand 2aCyclic peptide / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.48α = 90
b = 301.13β = 113.57
c = 145.37γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other