8SVM

Plasmodium falciparum M17 aminopeptidase bound to MMV1557817


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Characterisation of a novel antimalarial agent targeting haemaglobin digestion that shows cross-species reactivity and excellent in vivo properties.

de Koning-Ward, T.F.Drinkwater, N.Edgar, R.C.S.McGowan, S.Scammells, P.J.

(2024) mBio 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine aminopeptidase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
528Plasmodium falciparumMutation(s): 3 
Gene Names: LAPPF3D7_1446200
EC: 3.4.11.1 (PDB Primary Data), 3.4.13 (PDB Primary Data)
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WRC (Subject of Investigation/LOI)
Query on WRC

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BB [auth F]
EA [auth C]
EC [auth J]
IB [auth G]
LC [auth K]
BB [auth F],
EA [auth C],
EC [auth J],
IB [auth G],
LC [auth K],
NA [auth D],
P [auth A],
RB [auth H],
RC [auth L],
UA [auth E],
XB [auth I],
Y [auth B]
N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-3,3-dimethylbutanamide
C20 H21 F3 N2 O3
NRAVUPOEFDEIOQ-GOSISDBHSA-N
1PE
Query on 1PE

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AA [auth B]
AC [auth I]
CB [auth F]
DB [auth F]
FA [auth C]
AA [auth B],
AC [auth I],
CB [auth F],
DB [auth F],
FA [auth C],
FC [auth J],
GA [auth C],
GC [auth J],
HA [auth C],
JB [auth G],
KB [auth G],
MC [auth K],
OA [auth D],
PA [auth D],
Q [auth A],
R [auth A],
S [auth A],
SB [auth H],
SC [auth L],
TB [auth H],
TC [auth L],
UC [auth L],
VA [auth E],
WA [auth E],
XA [auth E],
YB [auth I],
Z [auth B],
ZB [auth I]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4
Query on SO4

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EB [auth F]
HC [auth J]
IA [auth C]
JA [auth C]
LB [auth G]
EB [auth F],
HC [auth J],
IA [auth C],
JA [auth C],
LB [auth G],
MB [auth G],
NB [auth G],
NC [auth K],
QA [auth D],
T [auth A],
U [auth A],
VC [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

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AB [auth F]
CA [auth C]
CC [auth J]
DA [auth C]
DC [auth J]
AB [auth F],
CA [auth C],
CC [auth J],
DA [auth C],
DC [auth J],
GB [auth G],
HB [auth G],
JC [auth K],
KC [auth K],
LA [auth D],
MA [auth D],
N [auth A],
O [auth A],
PB [auth H],
PC [auth L],
QB [auth H],
QC [auth L],
SA [auth E],
TA [auth E],
VB [auth I],
W [auth B],
WB [auth I],
X [auth B],
ZA [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
BA [auth C]
BC [auth J]
FB [auth G]
IC [auth K]
KA [auth D]
BA [auth C],
BC [auth J],
FB [auth G],
IC [auth K],
KA [auth D],
M [auth A],
OB [auth H],
OC [auth L],
RA [auth E],
UB [auth I],
V [auth B],
YA [auth F]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.204α = 90
b = 177.926β = 90
c = 229.762γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

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)Australia1185354

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release