5DZU

Structure of potato cathepsin D inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5DZU/pdb

• Classification: HYDROLASE INHIBITOR
• Organism(s): Solanum tuberosum
• Mutation(s): No 


• Deposited: 2015-09-26 Released: 2015-10-21 
• Deposition Author(s): Guo, J., Erskine, P., Coker, A.R., Wood, S.P., Cooper, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.270 
• R-Value Work: 0.191 
• R-Value Observed: 0.195 

Literature

Structure of a Kunitz-type potato cathepsin D inhibitor.

Guo, J., Erskine, P.T., Coker, A.R., Wood, S.P., Cooper, J.B.

(2015) J Struct Biol 192: 554-560

• PubMed: 26542926 
• DOI: https://doi.org/10.1016/j.jsb.2015.10.020
• Primary Citation of Related Structures:  
  5DZU


• PubMed Abstract: 
  

  Potato cathepsin D inhibitor (PDI) is a glycoprotein of 188 amino acids which can inhibit both the aspartic protease cathepsin D and the serine protease trypsin. Here we report the first X-ray structure of PDI at a resolution of 2.1 Å showing that PDI adopts a β-trefoil fold, which is typical of the Kunitz-family protease inhibitors, with the inhibitory loops protruding from the core. Possible reactive-site loops including one involving a unique disulphide and another involving a protruding 310 helix are identified and docking studies indicate the mode of action of this unusual bi-functional inhibitor.

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Organizational Affiliation: 

Division of Medicine, UCL, Gower Street, London WC1E 6BT, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.68 kDa 
• Atom Count: 2,947 
• Modelled Residue Count: 363 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartic protease inhibitor 11	A, B	188	Solanum tuberosum	Mutation(s): 0
UniProt
Find proteins for P16348 (Solanum tuberosum) Explore P16348  Go to UniProtKB:  P16348

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	C [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.270 
• R-Value Work: 0.191 
• R-Value Observed: 0.195 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.458	α = 90
b = 124.769	β = 95.14
c = 37.876	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Guo, J., Erskine, P., Coker, A.R., Wood, S.P., Cooper, J.B.

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2015-11-18
  Changes: Database references
• Version 1.2: 2015-11-25
  Changes: Database references
• Version 1.3: 2018-04-25
  Changes: Data collection
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary