1QTN | pdb_00001qtn

CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TETRAPEPTIDE INHIBITOR ACE-IETD-ALDEHYDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.188 (Depositor) 
  • R-Value Work: 
    0.143 (Depositor) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1QTN

This is version 1.6 of the entry. See complete history

Literature

The atomic-resolution structure of human caspase-8, a key activator of apoptosis.

Watt, W.Koeplinger, K.A.Mildner, A.M.Heinrikson, R.L.Tomasselli, A.G.Watenpaugh, K.D.

(1999) Structure 7: 1135-1143

  • DOI: https://doi.org/10.1016/s0969-2126(99)80180-4
  • Primary Citation Related Structures: 
    1QTN

  • PubMed Abstract: 

    Caspases are a family of cysteine proteases that have important intracellular roles in inflammation and apoptosis. Caspase-8 activates downstream caspases which are unable to carry out autocatalytic processing and activation. Caspase-8 is designated as an initiator caspase and is believed to sit at the apex of the Fas- or TNF-mediated apoptotic cascade. In view of this role, the enzyme is an attractive target for the design of inhibitors aimed at blocking the undesirable cell death associated with a range of degenerative disorders. The structure of recombinant human caspase-8, covalently modified with the inhibitor acetyl-Ile-Glu-Thr-Asp-aldehyde, has been determined by X-ray crystallography to 1.2 A resolution. The asymmetric unit contains the p18-p11 heterodimer; the biologically important molecule contains two dimers. The overall fold is very similar to that of caspase-1 and caspase-3, but significant differences exist in the substrate-binding region. The structure answers questions about the enzyme-inhibitor complex that could not be explained from earlier caspase structures solved at lower resolution. The catalytic triad in caspase-8 comprises Cys360, His317 and the backbone carbonyl oxygen atom of Arg258, which points towards the Nepsilon atom of His317. The oxygen atom attached to the tetrahedral carbon in the thiohemiacetal group of the inhibitor is hydrogen bonded to Ndelta of His317, and is not in a region characteristic of a classical 'oxyanion hole'. The N-acetyl group of the inhibitor is in the trans configuration. The caspase-8-inhibitor structure provides the basis for understanding structure/function relationships in this important initiator of the proteolytic cascade that leads to programmed cell death.


  • Organizational Affiliation
    • Structural, Analytical & Medicinal Chemistry Pharmacia & Upjohn Inc. 301 Henrietta Street, Kalamazoo, MI 49007, USA.

Macromolecule Content 

  • Total Structure Weight: 30.33 kDa 
  • Atom Count: 2,324 
  • Modeled Residue Count: 247 
  • Deposited Residue Count: 264 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CASPASE-8164Homo sapiensMutation(s): 0 
EC: 3.4.22 (PDB Primary Data), 3.4.22.61 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens)
Explore Q14790 
Go to UniProtKB:  Q14790
PHAROS:  Q14790
GTEx:  ENSG00000064012 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14790
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CASPASE-895Homo sapiensMutation(s): 0 
EC: 3.4.22 (PDB Primary Data), 3.4.22.61 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens)
Explore Q14790 
Go to UniProtKB:  Q14790
PHAROS:  Q14790
GTEx:  ENSG00000064012 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14790
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ACETYL-ILE-GLU-THR-ASP-ALDEHYDE5N/AMutation(s): 0 

Small Molecules

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.188 (Depositor) 
  • R-Value Work:  0.143 (Depositor) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.4α = 90
b = 62.4β = 90
c = 129.25γ = 120
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
SMARTdata reduction
SAINTdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-04-04
    Changes: Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 1.5: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2023-11-15
    Changes: Data collection