8T83 | pdb_00008t83

X-ray crystal structure of PfA-M1(M462K)

• PDB DOI: https://doi.org/10.2210/pdb8T83/pdb

• Classification: HYDROLASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-06-21 Released: 2024-06-26 
• Deposition Author(s): Yang, W., Drinkwater, N., Webb, C.T., McGowan, S.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Conformational dynamics of the Plasmodium falciparum M1 aminopeptidase.

Yang, W., Drinkwater, N., Webb, C.T., McGowan, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 105.17 kDa 
• Atom Count: 7,935 
• Modeled Residue Count: 889 
• Deposited Residue Count: 898 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase N	A	898	Plasmodium falciparum	Mutation(s): 1  Gene Names: M1AAP, MAL13P1.56, PF3D7_1311800 EC: 3.4.11
UniProt
Find proteins for O96935 (Plasmodium falciparum (isolate 3D7)) Explore O96935  Go to UniProtKB:  O96935

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.34	α = 90
b = 108.95	β = 90
c = 118.19	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Yang, W., Drinkwater, N., Webb, C.T., McGowan, S.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release