5JOD | pdb_00005jod

Structure of proplasmepsin IV from Plasmodium falciparum

PDB DOI: https://doi.org/10.2210/pdb5JOD/pdb
Entry: 5JOD supersedes: 4Y7H

Classification: HYDROLASE
Organism(s): Plasmodium falciparum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-05-02 Released: 2016-08-17
Deposition Author(s): Recacha, R., Akopjana, I., Tars, K., Jaudzems, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.209 (Depositor), 0.206 (DCC)
R-Value Work:
0.179 (Depositor), 0.177 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Plasmodium falciparum proplasmepsin IV: the plasticity of proplasmepsins.

Recacha, R., Jaudzems, K., Akopjana, I., Jirgensons, A., Tars, K.

(2016) Acta Crystallogr F Struct Biol Commun 72: 659-666

PubMed: 27599854 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X16011663
Primary Citation Related Structures:
5BWY, 5JOD

PubMed Abstract:
Plasmepsin IV from Plasmodium falciparum (PM IV) is a promising target for the development of novel antimalarial drugs. Here, the crystal structure of the truncated zymogen of PM IV (pPM IV), consisting of the mature enzyme plus a prosegment of 47 residues, has been determined at 1.5 Å resolution. pPM IV presents the fold previously described for studied proplasmepsins, displaying closer similarities to proplasmepin IV from P. vivax (pPvPM) than to the other two proplasmepsins from P. falciparum. The study and comparison of the pPM IV structure with the proplasmepsin structures described previously provide information about the similarities and differences in the inactivation-activation mechanisms among the plasmepsin zymogens.

Organizational Affiliation

Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia.

Macromolecule Content

Total Structure Weight: 85.57 kDa
Atom Count: 6,735
Modeled Residue Count: 750
Deposited Residue Count: 750
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proplasmepsin IV	A, B	375	Plasmodium falciparum	Mutation(s): 0 Gene Names: PFBG_05102
UniProt
Find proteins for W7FF86 (Plasmodium falciparum (isolate 7G8)) Explore W7FF86 Go to UniProtKB: W7FF86
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W7FF86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.209 (Depositor), 0.206 (DCC)
R-Value Work: 0.179 (Depositor), 0.177 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.909	α = 90
b = 62.78	β = 113.5
c = 94.03	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

This entry supersedes: 4Y7H

Revision History (Full details and data files)

Version 1.0: 2016-08-17
Type: Initial release
Version 1.1: 2016-09-14
Changes: Database references
Version 1.2: 2016-09-28
Changes: Database references
Version 1.3: 2018-01-17
Changes: Data collection
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.5: 2025-10-01
Changes: Advisory, Derived calculations, Structure summary