1W6I

plasmepsin II-pepstatin A complex

• PDB DOI: https://doi.org/10.2210/pdb1W6I/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Plasmodium falciparum, Streptomyces argenteolus subsp. toyonakensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-18 Released: 2006-07-05 
• Deposition Author(s): Lindberg, J., Johansson, P.-O., Rosenquist, A., Kvarnstroem, I., Vrang, L., Samuelsson, B., Unge, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.262 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Structural Study of a Novel Inhibitor with Bulky P1 Side Chain in Complex with Plasmepsin II -Implications for Drug Design

Lindberg, J., Johansson, P.-O., Rosenquist, A., Kvarnstroem, I., Vrang, L., Samuelsson, B., Unge, T.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.62 kDa 
• Atom Count: 5,542 
• Modelled Residue Count: 670 
• Deposited Residue Count: 674 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASMEPSIN 2 PRECURSOR	A, B [auth C]	331	Plasmodium falciparum	Mutation(s): 0  EC: 3.4.23.39
UniProt
Find proteins for P46925 (Plasmodium falciparum (isolate HB3)) Explore P46925  Go to UniProtKB:  P46925

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPSTATIN	C [auth B], D	6	Streptomyces argenteolus subsp. toyonakensis	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000557	C [auth B], D	Pepstatin	Oligopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.262 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.29	α = 90
b = 142.29	β = 90
c = 98.094	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-05 
Deposition Author(s): Lindberg, J., Johansson, P.-O., Rosenquist, A., Kvarnstroem, I., Vrang, L., Samuelsson, B., Unge, T.

Revision History  

• Version 1.0: 2006-07-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2013-03-06
  Changes: Other
• Version 1.3: 2017-02-08
  Changes: Source and taxonomy
• Version 1.4: 2018-01-17
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary