7RIE | pdb_00007rie

Plasmodium falciparum M17 in complex with inhibitor MIPS2571


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.229 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7RIE

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Genetic and chemical validation of Plasmodium falciparum aminopeptidase Pf A-M17 as a drug target in the hemoglobin digestion pathway.

Edgar, R.C.S.Siddiqui, G.Hjerrild, K.Malcolm, T.R.Vinh, N.B.Webb, C.T.Holmes, C.MacRaild, C.A.Chernih, H.C.Suen, W.W.Counihan, N.A.Creek, D.J.Scammells, P.J.McGowan, S.de Koning-Ward, T.F.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.80813
  • Primary Citation Related Structures: 
    7RIE

  • PubMed Abstract: 

    Plasmodium falciparum, the causative agent of malaria, remains a global health threat as parasites continue to develop resistance to antimalarial drugs used throughout the world. Accordingly, drugs with novel modes of action are desperately required to combat malaria. P. falciparum parasites infect human red blood cells where they digest the host's main protein constituent, hemoglobin. Leucine aminopeptidase Pf A-M17 is one of several aminopeptidases that have been implicated in the last step of this digestive pathway. Here, we use both reverse genetics and a compound specifically designed to inhibit the activity of Pf A-M17 to show that Pf A-M17 is essential for P. falciparum survival as it provides parasites with free amino acids for growth, many of which are highly likely to originate from hemoglobin. We further show that loss of Pf A-M17 results in parasites exhibiting multiple digestive vacuoles at the trophozoite stage. In contrast to other hemoglobin-degrading proteases that have overlapping redundant functions, we validate Pf A-M17 as a potential novel drug target.


  • Organizational Affiliation
    • School of Medicine, Deakin University, Geelong, Australia.

Macromolecule Content 

  • Total Structure Weight: 712.7 kDa 
  • Atom Count: 49,071 
  • Modeled Residue Count: 6,182 
  • Deposited Residue Count: 6,324 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
M17 leucyl aminopeptidase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
527Plasmodium falciparumMutation(s): 0 
EC: 3.4.11.1 (PDB Primary Data), 3.4.13 (UniProt)
UniProt
Find proteins for Q8IL11 (Plasmodium falciparum (isolate 3D7))
Explore Q8IL11 
Go to UniProtKB:  Q8IL11
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IL11
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5IF
(Subject of Investigation/LOI)

Query on 5IF



Download:Ideal Coordinates CCD File
AB [auth G]
BC [auth L]
DA [auth C]
FB [auth H]
HA [auth D]
AB [auth G],
BC [auth L],
DA [auth C],
FB [auth H],
HA [auth D],
KB [auth I],
OA [auth E],
PB [auth J],
Q [auth A],
TA [auth F],
VB [auth K],
W [auth B]
N-{(1R)-2-(hydroxyamino)-1-[4'-(hydroxymethyl)[1,1'-biphenyl]-4-yl]-2-oxoethyl}-2,2-dimethylpropanamide
C20 H24 N2 O4
RZJKOPJQCUYRDV-QGZVFWFLSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
AC [auth L]
BA [auth C]
CA [auth C]
JB [auth I]
NA [auth E]
AC [auth L],
BA [auth C],
CA [auth C],
JB [auth I],
NA [auth E],
OB [auth J],
P [auth A],
UB [auth K],
V [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth C]
EB [auth H]
LA [auth E]
MA [auth E]
SA [auth F]
AA [auth C],
EB [auth H],
LA [auth E],
MA [auth E],
SA [auth F],
TB [auth K],
U [auth B],
XA [auth G],
YA [auth G],
ZA [auth G],
ZB [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
CB [auth H]
DB [auth H]
FA [auth D]
GA [auth D]
HB [auth I]
CB [auth H],
DB [auth H],
FA [auth D],
GA [auth D],
HB [auth I],
IB [auth I],
JA [auth E],
KA [auth E],
MB [auth J],
N [auth A],
NB [auth J],
O [auth A],
QA [auth F],
RA [auth F],
RB [auth K],
S [auth B],
SB [auth K],
T [auth B],
VA [auth G],
WA [auth G],
XB [auth L],
Y [auth C],
YB [auth L],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3

Query on CO3



Download:Ideal Coordinates CCD File
BB [auth H]
EA [auth D]
GB [auth I]
IA [auth E]
LB [auth J]
BB [auth H],
EA [auth D],
GB [auth I],
IA [auth E],
LB [auth J],
M [auth A],
PA [auth F],
QB [auth K],
R [auth B],
UA [auth G],
WB [auth L],
X [auth C]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.229 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.29α = 90
b = 175.858β = 90
c = 234.679γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description