Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 154.83 kDa 
• Atom Count: 10646 
• Residue Count: 1306 
• Unique protein chains: 1

3QS1

Crystal structure of KNI-10006 complex of Plasmepsin I (PMI) from Plasmodium falciparum

• DOI: 10.2210/pdb3QS1/pdb

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


• Deposited: 2011-02-19 Released: 2011-05-11 
• Deposition Author(s): Bhaumik, P., Gustchina, A., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.300 
• R-Value Work: 0.211 
• R-Value Observed: 0.215 

Literature

Crystal structures of the free and inhibited forms of plasmepsin I (PMI) from Plasmodium falciparum.

Bhaumik, P., Horimoto, Y., Xiao, H., Miura, T., Hidaka, K., Kiso, Y., Wlodawer, A., Yada, R.Y., Gustchina, A.

(2011) J Struct Biol 175: 73-84

• PubMed: 21521654 
• DOI: 10.1016/j.jsb.2011.04.009
• Primary Citation of Related Structures:  
  3QS1, 3QRV


• PubMed Abstract: 
  

Plasmepsin I (PMI) is one of the four vacuolar pepsin-like proteases responsible for hemoglobin degradation by the malarial parasite Plasmodium falciparum, and the only one with no crystal structure reported to date. Due to substantial functional redundancy of these enzymes, lack of inhibition of even a single plasmepsin can defeat efforts in creating effective antiparasitic agents. We have now solved crystal structures of the recombinant PMI as apoenzyme and in complex with the potent peptidic inhibitor, KNI-10006, at the resolution of 2.4 and 3.1Å, respectively. The apoenzyme crystallized in the orthorhombic space group P2(1)2(1)2(1) with two molecules in the asymmetric unit and the structure has been refined to the final R-factor of 20.7%. The KNI-10006 bound enzyme crystallized in the tetragonal space group P4(3) with four molecules in the asymmetric unit and the structure has been refined to the final R-factor of 21.1%. In the PMI-KNI-10006 complex, the inhibitors were bound identically to all four enzyme molecules, with the opposite directionality of the main chain of KNI-10006 relative to the direction of the enzyme substrates. Such a mode of binding of inhibitors containing an allophenylnorstatine-dimethylthioproline insert in the P1-P1' positions, previously reported in a complex with PMIV, demonstrates the importance of satisfying the requirements for the proper positioning of the functional groups in the mechanism-based inhibitors towards the catalytic machinery of aspartic proteases, as opposed to binding driven solely by the specificity of the individual enzymes. A comparison of the structure of the PMI-KNI-10006 complex with the structures of other vacuolar plasmepsins identified the important differences between them and may help in the design of specific inhibitors targeting the individual enzymes.

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Organizational Affiliation: 

Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmepsin-1	A, B, C, D	336	Plasmodium falciparum	Mutation(s): 0  Gene Names: PMI EC: 3.4.23.38
Find proteins for P39898 (Plasmodium falciparum) Explore P39898  Go to UniProtKB:  P39898

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
006	A, B, C, D	(4R)-3-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide C35 H41 N3 O6 S KKTYZYHUPKXLPL-RIQJEONASA-N
GOL	A, B, C, D	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
6	Ki :  11   nM  PDBBind
006	IC50:  280   nM  BindingDB

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000575 (006)	A, B, C, D	KNI-10006	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.300 
• R-Value Work: 0.211 
• R-Value Observed: 0.215 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.69	α = 90
b = 93.69	β = 90
c = 160.12	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-19 
• Released Date: 2011-05-11 
Deposition Author(s): Bhaumik, P., Gustchina, A., Wlodawer, A.

Revision History 

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other