1LYW

CATHEPSIN D AT PH 7.5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Conformational switching in an aspartic proteinase.

Lee, A.Y., Gulnik, S.V., Erickson, J.W.

(1998) Nat Struct Biol 5: 866-871

  • DOI: 10.1038/2306
  • Primary Citation of Related Structures:  
    1LYW

  • PubMed Abstract: 

    • The crystal structure of a catalytically inactive form of cathepsin D (CatDhi) has been obtained at pH 7.5. The N-terminal strand relocates by 30 A from its position in the interdomain beta-sheet and inserts into the active site cleft, effectively blocki ...

    The crystal structure of a catalytically inactive form of cathepsin D (CatDhi) has been obtained at pH 7.5. The N-terminal strand relocates by 30 A from its position in the interdomain beta-sheet and inserts into the active site cleft, effectively blocking substrate access. CatDhi has a five-stranded interdomain beta-sheet and resembles Intermediate 3, a hypothetical structure proposed to be transiently formed during proteolytic activation of the proenzyme precursor. Interconversion between active and inactive forms of CatD is reversible and may be regulated by an ionizable switch involving the carboxylate side chains of Glu 5, Glu 180, and Asp 187. Our findings provide a structural basis for the pH-dependent regulation of aspartic proteinase activity and suggest a novel mechanism for pH-dependent modulation of substrate specificity.

    Related Citations: 
    • Crystal Structures of Native and Inhibited Forms of Human Cathepsin D: Implications for Lysosomal Targeting and Drug Design
      Baldwin, E.T., Bhat, T.N., Gulnik, S., Hosur, M.V., Sowder II, R.C., Cachau, R.E., Collins, J., Silva, A.M., Erickson, J.W.
      (1993) Proc Natl Acad Sci U S A 90: 6796
    • Human Liver Cathepsin D. Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of a Lysosomal Enzyme
      Gulnik, S., Baldwin, E.T., Tarasova, N., Erickson, J.
      (1992) J Mol Biol 227: 265
    Organizational Affiliation: 

    Structural Biochemistry Program, SAIC Frederick, National Cancer Institute, Maryland 21702-1201, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CATHEPSIN D A, C, E, G97Homo sapiensMutation(s): 0 
Gene Names: CTSD, CPSD
EC: 3.4.23.5
Find proteins for P07339 (Homo sapiens)
Explore P07339 
Go to UniProtKB:  P07339
NIH Common Fund Data Resources
PHAROS:  P07339
GTEx:  ENSG00000117984
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CATHEPSIN D B, D, F, H241Homo sapiensMutation(s): 0 
Gene Names: CTSD, CPSD
EC: 3.4.23.5
Find proteins for P07339 (Homo sapiens)
Explore P07339 
Go to UniProtKB:  P07339
NIH Common Fund Data Resources
PHAROS:  P07339
GTEx:  ENSG00000117984
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download Ideal Coordinates CCD File 
A, C, E, G
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.256α = 90
b = 136.797β = 90
c = 140.416γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-22
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance