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9yc0

Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3ab (MIPS3413)

Method: X-RAY DIFFRACTION D_max: 213.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yc0
deposition_date	2025-09-17
title	Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3ab (MIPS3413)
keywords	M17 aminopeptidase, aminopeptidase inhibitor, P. falciparum, malaria, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	71.67 Å
rg_electron	71.98 Å
i0	12914900000.00
molecular_weight	641820.0 kDa
excluded_volume	622680 Å³
envelope_volume	1162600 Å³
shell_volume	132960 Å³
envelope_diameter	247.0 Å
shell_rg	70.86 Å
envelope_rg	70.76 Å
shape_rg	72.00 Å
total_rg	71.93 Å
total_atoms	48352
n_residues	6167
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	213.2 Å
rg_real	71.64 Å
rg_real_error	1.28 Å
i0_real	1.2880e+10
i0_real_error	2.7340e+08
rg_reciprocal	70.39 Å
i0_reciprocal	12870000000.0000
total_estimate	0.8015
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	58.2 Å
skewness	0.391
kurtosis	-0.741
angular_range	— – 0.1100 Å⁻¹
current_alpha	0.0242
highest_alpha	1967000000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.814; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.001

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	M17 leucyl aminopeptidase
formula_weight	58577.8 kDa
ec_number	3.4.11.1
mutation	N152Q, N515Q, N546Q
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L
atom_count	51849

ASEVPQVVSLDPTSIPIEYNTPIHDIKVQVYDIKGGCNVEEGLTIFLVNNPGKENGPVKISSKVNDKQVSEFLKDENMEKFNVKLGTSKHFYMFNDNKNSVAVGYVGCGSVADLSEADMKRVVLSLVTMLHDNKLSKLTVVFEINVDKNLFRFFLETLFYEYMTDERFKSTDKNVNMEYIKHLGVYINNADTYKEEVEKARVYYFGTYYASQLIAAPSNYCNPVSLSNAAVELAQKLNLEYKILGVKELEELKMGAYLSVGKGSMYPNKFIHLTYKSKGDVKKKIALVGKGITFDSGGYNLKAAPGSMIDLMKFDMSGCAAVLGCAYCVGTLKPENVEIHFLSAVCENMVSKNSYRPGDIITASNGKTIEVGNTDAEGRLTLADALVYAEKLGVDYIVDIATLTGAMLYSLGTSYAGVFGNNEELINKILQSSKTSNEPVWWLPIINEYRATLNSKYADINQISSSVKASSIVASLFLKEFVQNTAWAHIDIAGVSWNFKARKPKGFGVRLLTEFVLNDALHHHHHH

Source

organism	Plasmodium falciparum
common_name	malaria parasite P. falciparum
ncbi_taxonomy_id	5833
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	24

Entity 3 non-polymer

description	CARBONATE ION
formula_weight	60.0 kDa
src_method	syn
entity_count	12

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	nat
entity_count	36

Entity 5 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	59

Entity 6 non-polymer

description	N-[(1R)-1-(1,3-benzothiazol-5-yl)-2-(hydroxyamino)-2-oxoethyl]-3,3-dimethylbutanamide
formula_weight	321.4 kDa
src_method	nat
entity_count	11

Entity 7 non-polymer

description	PENTAETHYLENE GLYCOL
formula_weight	238.3 kDa
src_method	syn
entity_count	37

Entity 8 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	13

Entity 9 non-polymer

description	NONAETHYLENE GLYCOL
formula_weight	414.5 kDa
src_method	nat
entity_count	2

Entity 10 non-polymer

description	N-[(1S)-1-(1,3-benzothiazol-5-yl)-2-(hydroxyamino)-2-oxoethyl]-3,3-dimethylbutanamide
formula_weight	321.4 kDa
src_method	nat
entity_count	1

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	3492

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6. Citations (1)

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length_a	173.729 Å
length_b	176.510 Å
length_c	231.308 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	48

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.370 Å
resolution_low	48.420 Å
r_factor	0.2212
r_work	0.2185
r_free	0.2708

fit	/app/data/saxs_computation/yc/9yc0/9yc0.fit
pddf	/app/data/pr_computation/yc/9yc0/9yc0.pr.out
profile	/app/data/saxs_computation/yc/9yc0/9yc0.dat