3CKI | pdb_00003cki

Crystal structure of the TACE-N-TIMP-3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.284 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structural determinants of the ADAM inhibition by TIMP-3: crystal structure of the TACE-N-TIMP-3 complex.

Wisniewska, M.Goettig, P.Maskos, K.Belouski, E.Winters, D.Hecht, R.Black, R.Bode, W.

(2008) J Mol Biology 381: 1307-1319

  • DOI: https://doi.org/10.1016/j.jmb.2008.06.088
  • Primary Citation Related Structures: 
    3CKI

  • PubMed Abstract: 

    TIMP-3 (tissue inhibitor of metalloproteinases 3) is unique among the TIMP inhibitors, in that it effectively inhibits the TNF-alpha converting enzyme (TACE). In order to understand this selective capability of inhibition, we crystallized the complex formed by the catalytic domain of recombinant human TACE and the N-terminal domain of TIMP-3 (N-TIMP-3), and determined its molecular structure with X-ray data to 2.3 A resolution. The structure reveals that TIMP-3 exhibits a fold similar to those of TIMP-1 and TIMP-2, and interacts through its functional binding edge, which consists of the N-terminal segment and other loops, with the active-site cleft of TACE in a manner similar to that of matrix metalloproteinases (MMPs). Therefore, the mechanism of TIMP-3 binding toward TACE is not fundamentally different from that previously elucidated for the MMPs. The Phe34 phenyl side chain situated at the tip of the relatively short sA-sB loop of TIMP-3 extends into a unique hydrophobic groove of the TACE surface, and two Leu residues in the adjacent sC-connector and sE-sF loops are tightly packed in the interface allowing favourable interactions, in agreement with predictions obtained by systematic mutations by Gillian Murphy's group. The combination of favourable functional epitopes together with a considerable flexibility renders TIMP-3 an efficient TACE inhibitor. This structure might provide means to design more efficient TIMP inhibitors of TACE.


  • Organizational Affiliation
    • Max-Planck-Institut für Biochemie, Proteinase Research Group, Am Klopferspitz 18, D-82152 Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 43.02 kDa 
  • Atom Count: 3,201 
  • Modeled Residue Count: 377 
  • Deposited Residue Count: 377 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ADAM 17256Homo sapiensMutation(s): 2 
Gene Names: ADAM17CSVPTACE
EC: 3.4.24.86
UniProt & NIH Common Fund Data Resources
Find proteins for P78536 (Homo sapiens)
Explore P78536 
Go to UniProtKB:  P78536
PHAROS:  P78536
GTEx:  ENSG00000151694 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78536
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Metalloproteinase inhibitor 3121Homo sapiensMutation(s): 0 
Gene Names: TIMP3
UniProt & NIH Common Fund Data Resources
Find proteins for P35625 (Homo sapiens)
Explore P35625 
Go to UniProtKB:  P35625
PHAROS:  P35625
GTEx:  ENSG00000100234 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35625
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.284 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.447α = 90
b = 70.447β = 90
c = 156.728γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary