PDB-9hb0: Crystal structure of Plasmodium falciparum Plasmepsin X in comple...

ID or keywords:

Entry

Database: PDB / ID: 9hb0

Title

Crystal structure of Plasmodium falciparum Plasmepsin X in complex with the hydroxyethylamine drug 7k.

Components

Plasmepsin X

Keywords

HYDROLASE / Aspartyl protease / hydroxyethylamine inhibitor / complex / non-covalent.

Function / homology

Function and homology information

MHC class II antigen presentation / Neutrophil degranulation / entry into host cell by a symbiont-containing vacuole / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / protein autoprocessing / transport vesicle / protein processing / aspartic-type endopeptidase activity / lysosome / proteolysis
Similarity search - Function

Biological species

Plasmodium falciparum 3D7 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Withers-Martinez, C. / George, R. / Ogrodowicz, R. / Kunzelmann, S. / Purkiss, A. / Kjaer, S. / Walker, P. / Kovada, V. / Jirgensons, A. / Blackman, M.J.

Funding support

United Kingdom, 2items

Citation

Journal: J.Mol.Biol. / Year: 2025
Title: Structural Plasticity of Plasmodium falciparum Plasmepsin X to Accommodate Binding of Potent Macrocyclic Hydroxyethylamine Inhibitors.
Authors: Withers-Martinez, C. / George, R. / Ogrodowicz, R. / Kunzelmann, S. / Purkiss, A.G. / Kjaer, S. / Walker, P.A. / Kovada, V. / Jirgensons, A. / Blackman, M.J.

History

Deposition	Nov 5, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 19, 2025	Provider: repository / Type: Initial release
Revision 1.1	Mar 26, 2025	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9hb0.cif.gz	323.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9hb0_validation.pdf.gz	782.7 KB	Display	wwPDB validaton report
Full document	9hb0_full_validation.pdf.gz	789.9 KB	Display
Data in XML	9hb0_validation.xml.gz	19.6 KB	Display
Data in CIF	9hb0_validation.cif.gz	27.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hb/9hb0 ftp://data.pdbj.org/pub/pdb/validation_reports/hb/9hb0	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Plasmepsin X

hetero molecules

41.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: surface plasmon resonance

Unit cell

Length a, b, c (Å)	147.95, 147.95, 147.95
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	197
Space group name H-M	I23

Components on special symmetry positions

ID	Model	Components
1	1	A-753- HOH

#1: Protein	Plasmepsin X / PfPMX / Plasmepsin 10 Mass: 40426.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PMX, PF3D7_0808200 Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: Q8IAS0, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Chemical	ChemComp-A1ITU / (4S)-4-[(1R)-2-[2-(3-methoxyphenyl)propan-2-ylamino]-1-oxidanyl-ethyl]-16-propyl-3,16-diazatricyclo[16.3.1.1^{6,10}]tricosa-1(21),6,8,10(23),18(22),19-hexaene-2,17-dione Mass: 585.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₆H₄₇N₃O₄
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.34 Å³/Da / Density % sol: 63.2 %
Crystal grow	Temperature: 293.15 K / Method: evaporation Details: 20% [w/v] PEG 4000, 0.2 M Magnesium sulfate, 10% [w/v] Glycerol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.7→104.62 Å / Num. obs: 59002 / % possible obs: 100 % / Redundancy: 40.4 % / CC_1/2: 1 / R_merge(I) obs: 0.1 / R_pim(I) all: 0.022 / R_rim(I) all: 0.102 / Net I/σ(I): 22.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
9-104.62	37	0.042	447	0.999	0.009	0.043
1.7-1.73	40.2	6.873	3126	0.303	1.557	7.047

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
Aimless		data scaling
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→104.616 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.945 / SU B: 4.823 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2265	2835	4.806 %
R_work	0.1952	56157	-
all	0.197	-	-
obs	-	58992	99.997 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 42.21 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.7→104.616 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2538	0	48	199	2785

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	2800
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	2491
X-RAY DIFFRACTION	r_angle_refined_deg	2.067	1.801	3828
X-RAY DIFFRACTION	r_angle_other_deg	0.824	1.715	5760
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.795	5	357
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.92	9.688	16
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	6.36	5	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.084	10	426
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.786	10	123
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	420
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3286
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	650
X-RAY DIFFRACTION	r_nbd_refined	0.187	0.2	448
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	2202
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	1311
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	1451
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.248	0.2	169
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.438	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.149	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.083	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	3.152	2.827	1386
X-RAY DIFFRACTION	r_mcbond_other	3.15	2.827	1386
X-RAY DIFFRACTION	r_mcangle_it	4.333	5.06	1745
X-RAY DIFFRACTION	r_mcangle_other	4.335	5.063	1746
X-RAY DIFFRACTION	r_scbond_it	4.146	3.146	1414
X-RAY DIFFRACTION	r_scbond_other	4.121	3.138	1411
X-RAY DIFFRACTION	r_scangle_it	5.895	5.637	2079
X-RAY DIFFRACTION	r_scangle_other	5.866	5.621	2074
X-RAY DIFFRACTION	r_lrange_it	8.29	29.087	3000
X-RAY DIFFRACTION	r_lrange_other	8.258	27.707	2953

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.7-1.744	0.327	210	0.361	4101	0.359	4311	0.914	0.904	100	0.359
1.744-1.792	0.332	218	0.323	4004	0.324	4222	0.925	0.933	100	0.314
1.792-1.844	0.334	207	0.286	3882	0.288	4089	0.94	0.948	100	0.267
1.844-1.901	0.266	183	0.257	3815	0.258	3998	0.954	0.958	100	0.227
1.901-1.963	0.249	222	0.229	3656	0.23	3878	0.96	0.966	100	0.197
1.963-2.032	0.216	146	0.217	3607	0.217	3753	0.969	0.97	100	0.185
2.032-2.109	0.259	151	0.213	3452	0.215	3603	0.959	0.971	100	0.182
2.109-2.195	0.211	190	0.198	3310	0.198	3500	0.972	0.976	100	0.17
2.195-2.292	0.213	170	0.192	3188	0.193	3358	0.97	0.977	100	0.165
2.292-2.404	0.226	160	0.193	3015	0.194	3175	0.972	0.977	100	0.168
2.404-2.534	0.237	133	0.191	2913	0.193	3046	0.964	0.977	100	0.168
2.534-2.688	0.232	125	0.195	2788	0.196	2913	0.971	0.976	100	0.176
2.688-2.873	0.23	128	0.191	2557	0.193	2685	0.969	0.978	100	0.176
2.873-3.103	0.217	131	0.187	2429	0.188	2560	0.971	0.979	100	0.177
3.103-3.399	0.198	103	0.188	2212	0.188	2315	0.977	0.98	100	0.187
3.399-3.8	0.24	87	0.18	2037	0.182	2124	0.967	0.981	100	0.19
3.8-4.387	0.155	75	0.169	1809	0.168	1884	0.985	0.983	100	0.191
4.387-5.37	0.194	89	0.15	1503	0.152	1592	0.98	0.987	100	0.182
5.37-7.585	0.256	54	0.22	1205	0.221	1259	0.974	0.977	100	0.261
7.585-104.616	0.313	53	0.233	674	0.238	729	0.928	0.964	99.7257	0.309

Refinement TLS params.

Method: refined / Origin x: 62.9095 Å / Origin y: 24.0416 Å / Origin z: -20.8567 Å

	11	12	13	21	22	23	31	32	33
T	0.0329 Å²	0.0196 Å²	-0.0119 Å²	-	0.0796 Å²	0.0015 Å²	-	-	0.0213 Å²
L	2.5224 °²	0.1668 °²	1.0357 °²	-	1.0967 °²	0.5496 °²	-	-	1.3684 °²
S	-0.0173 Å °	-0.2871 Å °	-0.1103 Å °	-0.0964 Å °	-0.0238 Å °	0.1107 Å °	-0.0563 Å °	-0.2808 Å °	0.0411 Å °

Refinement TLS group

Selection: ALL

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