Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 75.84 kDa 
• Atom Count: 5399 
• Residue Count: 674 
• Unique protein chains: 2

2R9B

Structural Analysis of Plasmepsin 2 from Plasmodium falciparum complexed with a peptide-based inhibitor

• DOI: 10.2210/pdb2R9B/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-12 Released: 2007-11-27 
• Deposition Author(s): Liu, P., Marzahn, M.R., Robbins, A.H., McKenna, R., Dunn, B.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.286 
• R-Value Work: 0.238 
• R-Value Observed: 0.271 

Literature

Recombinant plasmepsin 1 from the human malaria parasite plasmodium falciparum: enzymatic characterization, active site inhibitor design, and structural analysis.

Liu, P., Marzahn, M.R., Robbins, A.H., Gutierrez-de-Teran, H., Rodriguez, D., McClung, S.H., Stevens, S.M., Yowell, C.A., Dame, J.B., McKenna, R., Dunn, B.M.

(2009) Biochemistry 48: 4086-4099

• PubMed: 19271776 
• DOI: 10.1021/bi802059r
• Primary Citation of Related Structures:  
  2R9B


• PubMed Abstract: 
  

A mutated form of truncated proplasmepsin 1 (proPfPM1) from the human malaria parasite Plasmodium falciparum, proPfPM1 K110pN, was generated and overexpressed in Escherichia coli. The automaturation process was carried out at pH 4.0 and 4.5, and the optimal catalytic pH of the resulting mature PfPM1 was determined to be pH 5.5. This mature PfPM1 showed comparable binding affinity to peptide substrates and inhibitors with the naturally occurring form isolated from parasites. The S3-S3' subsite preferences of the recombinant mature PfPM1 were explored using combinatorial chemistry based peptide libraries. On the basis of the results, a peptidomimetic inhibitor (compound 1) was designed and yielded 5-fold selectivity for binding to PfPM1 versus the homologous human cathepsin D (hcatD). The 2.8 A structure of the PfPM2-compound 1 complex is reported. Modeling studies were conducted using a series of peptidomimetic inhibitors (compounds 1-6, Table 3) and three plasmepsins: the crystal structure of PfPM2, and homology derived models of PfPM1 and PfPM4.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida 32610-0245, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmepsin-2	A, B	329	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: plasmepsin 2 EC: 3.4.23.39
Find proteins for P46925 (Plasmodium falciparum) Explore P46925  Go to UniProtKB:  P46925

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide-based inhibitor	C, D	8	N/A	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000306	C, D	KPFS-(CH2-NH)-LQF peptidomimetic inhibitor of PfPM1	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.286 
• R-Value Work: 0.238 
• R-Value Observed: 0.271 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 219.489	α = 90
b = 69.032	β = 102.85
c = 53.578	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-09-12 
• Released Date: 2007-11-27 
Deposition Author(s): Liu, P., Marzahn, M.R., Robbins, A.H., McKenna, R., Dunn, B.M.

Revision History 

• Version 1.0: 2007-11-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2011-08-17
  Changes: Non-polymer description
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2017-10-25
  Changes: Refinement description