5Y1H | pdb_00005y1h

Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(2,4-difluorobenzyl)ureido)-N-hydroxy-4-methylpentanamide

• PDB DOI: https://doi.org/10.2210/pdb5Y1H/pdb

• Classification: HYDROLASE
• Organism(s): Plasmodium falciparum FcB1/Columbia
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-20 Released: 2018-08-01 
• Deposition Author(s): Marapaka, A.K., Zhang, Y., Addlagatta, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(2,4-difluorobenzyl)ureido)-N-hydroxy-4-methylpentanamide

Marapaka, A.K., Addlagatta, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 107.02 kDa 
• Atom Count: 7,955 
• Modeled Residue Count: 890 
• Deposited Residue Count: 914 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M1 family aminopeptidase	A	914	Plasmodium falciparum FcB1/Columbia	Mutation(s): 0  EC: 3.4.11
UniProt
Find proteins for O96935 (Plasmodium falciparum (isolate 3D7)) Explore O96935  Go to UniProtKB:  O96935

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E8C (Subject of Investigation/LOI)	I [auth A]	(2R)-2-[[2,4-bis(fluoranyl)phenyl]methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide C14 H19 F2 N3 O3 IJLRZCJOVWWKMB-GFCCVEGCSA-N
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.564	α = 90
b = 109.241	β = 90
c = 112.518	γ = 90

Software Package:

Software Name	Purpose
DENZO	data collection
SCALEPACK	data scaling
MOLREP	model building
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Marapaka, A.K., Zhang, Y., Addlagatta, A.

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description