Crystal structure of TACE in complex with JMV 390-1

Experimental Data Snapshot

  • Resolution: 2.02 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

Starting Model: experimental
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Stabilization of the autoproteolysis of TNF-alpha converting enzyme (TACE) results in a novel crystal form suitable for structure-based drug design studies.

Ingram, R.N.Orth, P.Strickland, C.L.Le, H.V.Madison, V.Beyer, B.M.

(2006) Protein Eng Des Sel 19: 155-161

  • DOI: https://doi.org/10.1093/protein/gzj014
  • Primary Citation of Related Structures:  
    2DDF, 2FV9

  • PubMed Abstract: 

    The crystallization of TNF-alpha converting enzyme (TACE) has been useful in understanding the structure-activity relationships of new chemical entities. However, the propensity of TACE to undergo autoproteolysis has made enzyme handling difficult and impeded the identification of inhibitor soakable crystal forms. The autoproteolysis of TACE was found to be specific (Y352-V353) and occurred within a flexible loop that is in close proximity to the P-side of the active site. The rate of autoproteolysis was found to be proportional to the concentration of TACE, suggesting a bimolecular reaction mechanism. A limited specificity study of the S(1)' subsite was conducted using surrogate peptides and suggested substitutions that would stabilize the proteolysis of the loop at positions Y352-V353. Two mutant proteases (V353G and V353S) were generated and proved to be highly resistant to autoproteolysis. The kinetics of the more resistant mutant (V353G) and wild-type TACE were compared and demonstrated virtually identical IC(50) values for a panel of competitive inhibitors. However, the k(cat)/K(m) of the mutant for a larger substrate (P6 - P(6)') was approximately 5-fold lower than that for the wild-type enzyme. Comparison of the complexed wild-type and mutant structures indicated a subtle shift in a peripheral P-side loop (comprising the mutation site) that may be involved in substrate binding/turnover and might explain the mild kinetic difference. The characterization of this stabilized form of TACE has yielded an enzyme with similar native kinetic properties and identified a novel crystal form that is suitable for inhibitor soaking and structure determination.

  • Organizational Affiliation

    Department of Structural Chemistry, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
258Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for P78536 (Homo sapiens)
Explore P78536 
Go to UniProtKB:  P78536
GTEx:  ENSG00000151694 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78536
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 002

Download Ideal Coordinates CCD File 
C23 H35 N3 O6
Query on INN

Download Ideal Coordinates CCD File 
D [auth A]N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-3-methyl-L-valyl-N-(2-aminoethyl)-L-alaninamide
C19 H37 N5 O5
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.02 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.799α = 90
b = 76.221β = 90
c = 102.092γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2006-03-14 
  • Deposition Author(s): Orth, P.

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other
  • Version 1.4: 2017-02-01
    Changes: Structure summary
  • Version 1.5: 2017-10-18
    Changes: Refinement description
  • Version 1.6: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.7: 2023-08-30
    Changes: Data collection, Refinement description