1ROA

Structure of human cystatin D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human cystatin D, a cysteine peptidase inhibitor with restricted inhibition profile.

Alvarez-Fernandez, M.Liang, Y.H.Abrahamson, M.Su, X.D.

(2005) J.Biol.Chem. 280: 18221-18228

  • DOI: 10.1074/jbc.M411914200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cystatins are natural inhibitors of papain-like (family C1) and legumain-related (family C13) cysteine peptidases. Cystatin D is a type 2 cystatin, a secreted inhibitor found in human saliva and tear fluid. Compared with its homologues, cystatin D pr ...

    Cystatins are natural inhibitors of papain-like (family C1) and legumain-related (family C13) cysteine peptidases. Cystatin D is a type 2 cystatin, a secreted inhibitor found in human saliva and tear fluid. Compared with its homologues, cystatin D presents an unusual inhibition profile with a preferential inhibition cathepsin S > cathepsin H > cathepsin L and no inhibition of cathepsin B or pig legumain. To elucidate the structural reasons for this specificity, we have crystallized recombinant human Arg(26)-cystatin D and solved its structures at room temperature and at cryo conditions to 2.5- and 1.8-A resolution, respectively. Human cystatin D presents the typical cystatin fold, with a five-stranded anti-parallel beta-sheet wrapped around a five-turn alpha-helix. The structures reveal differences in the peptidase-interacting regions when compared with other cystatins, providing plausible explanations for the restricted inhibitory specificity of cystatin D for some papain-like peptidases and its lack of reactivity toward legumain-related enzymes.


    Organizational Affiliation

    Department of Clinical Chemistry, Institute of Laboratory Medicine, Lund University, SE-221 85 Lund, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cystatin D
A
122Homo sapiensMutation(s): 1 
Gene Names: CST5
Find proteins for P28325 (Homo sapiens)
Go to Gene View: CST5
Go to UniProtKB:  P28325
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.250 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 34.050α = 90.00
b = 81.720β = 90.00
c = 46.740γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Data collection, Refinement description