Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.93 kDa 
• Atom Count: 944 
• Residue Count: 112 
• Unique protein chains: 1

1RN7

Structure of human cystatin D

• DOI: 10.2210/pdb1RN7/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-11-30 Released: 2004-05-18 
• Deposition Author(s): Alvarez-Fernandez, M., Liang, Y.H., Abrahamson, M., Su, X.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.229 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 

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

• PubMed: 15728581 
• DOI: 10.1074/jbc.M411914200
• Primary Citation of Related Structures:  
  1RN7, 1ROA


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystatin D	A	122	Homo sapiens	Mutation(s): 1  Gene Names: CST5
Find proteins for P28325 (Homo sapiens) Explore P28325  Go to UniProtKB:  P28325
NIH Common Fund Data Resources
PHAROS  P28325 GTEx  ENSG00000170367

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.229 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.9	α = 90
b = 84.37	β = 90
c = 47.65	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-30 
• Released Date: 2004-05-18 
Deposition Author(s): Alvarez-Fernandez, M., Liang, Y.H., Abrahamson, M., Su, X.D.

Revision History 

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