1M43

Crystal structure of PMII in complex with pepstatin a to 2.4 A

• PDB DOI: https://doi.org/10.2210/pdb1M43/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Plasmodium falciparum, Streptomyces argenteolus subsp. toyonakensis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-07-02 Released: 2002-07-24 
• Deposition Author(s): Asojo, O.A., Silva, A.M., Gulnik, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.245 (Depositor) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Novel uncomplexed and complex structures of PM II, an aspartic protease from P. falciparum

Asojo, O.A., Silva, A.M., Gulnik, S.

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: 75.53 kDa 
• Atom Count: 5,885 
• Modelled Residue Count: 674 
• Deposited Residue Count: 674 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
plasmepsin II	A, B	331	Plasmodium falciparum	Mutation(s): 1  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, 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, D	Pepstatin	Oligopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.245 (Depositor) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.235	α = 90
b = 142.235	β = 90
c = 97.892	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-24 
Deposition Author(s): Asojo, O.A., Silva, A.M., Gulnik, S.

Revision History  

• Version 1.0: 2002-07-24
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2013-02-27
  Changes: Other
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary