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9yc7

Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3k (MIPS3415)

Method: X-RAY DIFFRACTION D_max: 211.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yc7
deposition_date	2025-09-18
title	Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3k (MIPS3415)
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	71.63 Å
rg_electron	71.91 Å
i0	12719600000.00
molecular_weight	639010.0 kDa
excluded_volume	621110 Å³
envelope_volume	1174100 Å³
shell_volume	134660 Å³
envelope_diameter	247.6 Å
shell_rg	70.70 Å
envelope_rg	70.55 Å
shape_rg	71.93 Å
total_rg	71.87 Å
total_atoms	48235
n_residues	6155
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	211.1 Å
rg_real	71.52 Å
rg_real_error	1.21 Å
i0_real	1.2680e+10
i0_real_error	2.7250e+08
rg_reciprocal	70.39 Å
i0_reciprocal	12680000000.0000
total_estimate	0.5764
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	57.6 Å
skewness	0.391
kurtosis	-0.727
angular_range	— – 0.1100 Å⁻¹
current_alpha	0.0206
highest_alpha	1802000000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 0.998; Sysdev: 0.006; Positv: 1.000; Valcen: 0.972; Smooth: 0.001

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	M17 leucyl aminopeptidase
formula_weight	58577.8 kDa
ec_number	3.4.11.1
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	50351

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	43

Entity 5 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	19

Entity 6 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	23

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	nat
entity_count	2

Entity 8 non-polymer

description	N-[(1R)-2-(hydroxyamino)-2-oxo-1-(quinolin-7-yl)ethyl]-3,3-dimethylbutanamide
formula_weight	315.4 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	PENTAETHYLENE GLYCOL
formula_weight	238.3 kDa
src_method	syn
entity_count	7

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2098

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6. Citations (1)

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length_a	173.842 Å
length_b	177.515 Å
length_c	230.510 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	48.300 Å
r_factor	0.2504
r_work	0.2485
r_free	0.2866

fit	/app/data/saxs_computation/yc/9yc7/9yc7.fit
pddf	/app/data/pr_computation/yc/9yc7/9yc7.pr.out
profile	/app/data/saxs_computation/yc/9yc7/9yc7.dat