5DZU | pdb_00005dzu

Structure of potato cathepsin D inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.270 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1016/j.jsb.2015.10.020
  • Primary Citation 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.

    • Organizational Affiliation: 
    • Division of Medicine, UCL, Gower Street, London WC1E 6BT, United Kingdom.

Macromolecule Content 

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

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aspartic protease inhibitor 11
A, B
188Solanum tuberosumMutation(s): 0 
UniProt
Find proteins for P16348 (Solanum tuberosum)
Explore P16348 
Go to UniProtKB:  P16348
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16348
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.458α = 90
b = 124.769β = 95.14
c = 37.876γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.6: 2024-10-16
    Changes: Structure summary