1XE5 | pdb_00001xe5

Structure of plasmepsin II in complex of an pepstatin analogue

• PDB DOI: https://doi.org/10.2210/pdb1XE5/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Plasmodium falciparum
• Mutation(s): No 


• Deposited: 2004-09-09 Released: 2005-08-23 
• Deposition Author(s): Prade, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Structure of plasmepsin II in complex of an pepstatin analogue

Prade, L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 75.35 kDa 
• Atom Count: 5,544 
• Modeled Residue Count: 658 
• Deposited Residue Count: 658 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmepsin 2	A, B	329	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5FE	C [auth A], D [auth B]	5,5,5-TRIFLUORO-3-HYDROXY-4-[2-(5,5,5-TRIFLUORO-3-HYDROXY-4-{3-METHYL-2-[3-METHYL-2-(3-METHYL-BUTYRYLAMINO)-BUTYRYLAMINO]-BUTYRYLAMINO}-PENTANOYLAMINO)-PROPIONYLAMINO]-PENTANOIC ACID METHYL ESTER C29 H47 F6 N5 O9 DBMUWIXNLHQYDY-OCVHHRCCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000639 (5FE)	C [auth A], D [auth B]	bis-trifluoromethyl pepstatin A ester analogue	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.65	α = 90
b = 141.65	β = 90
c = 98.35	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-23 
Deposition Author(s): Prade, L.

Revision History  

• Version 1.0: 2005-08-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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: 2012-12-12
  Changes: Other
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary