5Y1Q

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

• PDB DOI: https://doi.org/10.2210/pdb5Y1Q/pdb

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


• Deposited: 2017-07-21 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: 2.14 Å
• R-Value Free: 0.219 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Development of peptidomimetic hydroxamates as PfA-M1 and PfA-M17 dual inhibitors: Biological evaluation and structural characterization by cocrystallization

Marapaka, A.K., Sankoju, P., Zhang, G., Ding, Y., Ma, C., Pillalamarri, V., Sudhakar, P., Reddi, B., Sijwali, P.S., Zhang, Y., Addlagatta, A.

(2022) Chin Chem Lett 33: 2550-2554

• DOI: https://doi.org/10.1016/j.cclet.2021.09.102

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: 106.74 kDa 
• Atom Count: 7,655 
• Modelled 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8L0 (Subject of Investigation/LOI)	F [auth A]	(2S)-2-[(3-chlorophenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide C14 H20 Cl N3 O3 RWIGPNFZQZONOD-LBPRGKRZSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.219 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.128	α = 90
b = 109.609	β = 90
c = 113.138	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: 2022-07-27
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-22
  Changes: Data collection, Refinement description