1XDH | pdb_00001xdh

Structure of plasmepsin II in complex with pepstatin A

• PDB DOI: https://doi.org/10.2210/pdb1XDH/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Plasmodium falciparum, Streptomyces argenteolus subsp. toyonakensis
• Mutation(s): No 


• Deposited: 2004-09-06 Released: 2005-08-23 
• Deposition Author(s): Prade, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.237 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Structure of plasmepsin II in complex with pepstatin A

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: 75.62 kDa 
• Atom Count: 6,046 
• Modeled Residue Count: 670 
• Deposited Residue Count: 674 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmepsin 2	A, B	331	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

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: 1.70 Å
• R-Value Free:  0.237 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.111	α = 90
b = 141.111	β = 90
c = 97.102	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: 2013-02-27
  Changes: Other
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary