1ME6 | pdb_00001me6

CRYSTAL STRUCTURE OF PLASMEPSIN II, AN ASPARTYL PROTEASE FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH A STATINE-BASED INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb1ME6/pdb

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


• Deposited: 2002-08-08 Released: 2004-01-20 
• Deposition Author(s): Freire, E., Nezami, A.G., Amzel, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.271 (Depositor) 
• R-Value Work: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF PLASMEPSIN II, AN ASPARTYL PROTEASE FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH A STATINE-BASED INHIBITOR

Freire, E., Nezami, A.G., Amzel, L.M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (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: 74.88 kDa 
• Atom Count: 5,402 
• Modeled Residue Count: 658 
• Deposited Residue Count: 658 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmepsin II	A, B	329	Plasmodium falciparum	Mutation(s): 0  Gene Names: PF00026 EC: 3.4.23.39
UniProt
Find proteins for P46925 (Plasmodium falciparum (isolate HB3)) Explore P46925  Go to UniProtKB:  P46925

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IVS	C [auth A], D [auth B]	3-HYDROXY-6-METHYL-4-(3-METHYL-2-(3-METHYL-2-(3-METHYL-BUTYRYLAMINO)-BUTYRYLAMINO)-BUTYRYLAMINO)-HEPTANOIC ACID ETHYL ESTER C25 H47 N3 O6 SMVMSLPPAGGLDL-ZZTDLJEGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.271 (Depositor) 
• R-Value Work:  0.214 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.93	α = 90
b = 141.93	β = 90
c = 97.82	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-20 
Deposition Author(s): Freire, E., Nezami, A.G., Amzel, L.M.

Revision History  

• Version 1.0: 2004-01-20
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary