7TBB | pdb_00007tbb

Crystal structure of Plasmepsin X from Plasmodium falciparum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7TBB

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Basis for drug selectivity of plasmepsin IX and X inhibition in Plasmodium falciparum and vivax.

Hodder, A.N.Christensen, J.Scally, S.Triglia, T.Ngo, A.Birkinshaw, R.W.Bailey, B.Favuzza, P.Dietrich, M.H.Tham, W.H.Czabotar, P.E.Lowes, K.Guo, Z.Murgolo, N.Lera Ruiz, M.McCauley, J.A.Sleebs, B.E.Olsen, D.Cowman, A.F.

(2022) Structure 30: 947

  • DOI: https://doi.org/10.1016/j.str.2022.03.018
  • Primary Citation Related Structures: 
    7TBB, 7TBC, 7TBD, 7TBE

  • PubMed Abstract: 

    Plasmepsins IX (PMIX) and X (PMX) are essential aspartyl proteases for Plasmodium spp. egress, invasion, and development. WM4 and WM382 inhibit PMIX and PMX in Plasmodium falciparum and P. vivax. WM4 inhibits PMX, while WM382 is a dual inhibitor of PMIX and PMX. To understand their function, we identified protein substrates. Enzyme kinetic and structural analyses identified interactions responsible for drug specificity. PMIX and PMX have similar substrate specificity; however, there are distinct differences for peptide and protein substrates. Differences in WM4 and WM382 binding for PMIX and PMX map to variations in the S' region and engagement of the active site S3 pocket. Structures of PMX reveal interactions and mechanistic detail of drug binding important for development of clinical candidates against these targets.


  • Organizational Affiliation
    • The Walter and Eliza Hall Institute of Medical Research, Parkville 3052 VIC, Australia; University of Melbourne, Melbourne, 3010 VIC, Australia.

Macromolecule Content 

  • Total Structure Weight: 43.73 kDa 
  • Atom Count: 2,823 
  • Modeled Residue Count: 332 
  • Deposited Residue Count: 377 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Plasmepsin 10377Plasmodium falciparumMutation(s): 0 
EC: 3.4.23
UniProt
Find proteins for Q8IAS0 (Plasmodium falciparum (isolate 3D7))
Explore Q8IAS0 
Go to UniProtKB:  Q8IAS0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IAS0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
C [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.308α = 90
b = 63.152β = 90
c = 79.337γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom109662/Z/15/Z, 202749/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary