SAXSdb — 9y65

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1. Structure Basics

entry_id	9y65
deposition_date	2025-09-08
title	Plasmodium falciparum M1 aminopeptidase (PfA-M1) bound to inhibitor 3k (MIPS3415)
keywords	M1 aminopeptidase, M1 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	28.81 Å
rg_electron	28.14 Å
i0	306225000.00
molecular_weight	94897.0 kDa
excluded_volume	92487 Å³
envelope_volume	151550 Å³
shell_volume	43290 Å³
envelope_diameter	99.8 Å
shell_rg	36.81 Å
envelope_rg	28.25 Å
shape_rg	28.15 Å
total_rg	28.67 Å
total_atoms	7188
n_residues	890
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	91.2 Å
rg_real	28.70 Å
rg_real_error	0.52 Å
i0_real	3.0620e+08
i0_real_error	4.2180e+06
rg_reciprocal	28.75 Å
i0_reciprocal	306200000.0000
total_estimate	0.8896
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.5 Å
skewness	0.277
kurtosis	-0.253
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	54660000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.949

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Plasmodium falciparum M1 aminopeptidase (PfA-M1)
formula_weight	126267.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7663

MKLTKGCAYKYIIFTVLILANILYDNKKRCMIKKNLRISSCGIISRLLKSNSNYNSFNKNYNFTSAISELQFSNFWNLDILQKDIFSNIHNNKNKPQSYIIHKRLMSEKGDNNNNNHQNNNGNDNKKRLGSVVNNEENTCSDKRMKPFEEGHGITQVDKMNNNSDHLQQNGVMNLNSNNVENNNNNNSVVVKKNEPKIHYRKDYKPSGFIINQVTLNINIHDQETIVRSVLDMDISKHNVGEDLVFDGVGLKINEISINNKKLVEGEEYTYDNEFLTIFSKFVPKSKFAFSSEVIIHPETNYALTGLYKSKNIIVSQCEATGFRRITFFIDRPDMMAKYDVTVTADKEKYPVLLSNGDKVNEFEIPGGRHGARFNDPPLKPCYLFAVVAGDLKHLSATYITKYTKKKVELYVFSEEKYVSKLQWALECLKKSMAFDEDYFGLEYDLSRLNLVAVSDFNVGAMENKGLNIFNANSLLASKKNSIDFSYARILTVVGHEYFHQYTGNRVTLRDWFQLTLKEGLTVHRENLFSEEMTKTVTTRLSHVDLLRSVQFLEDSSPLSHPIRPESYVSMENFYTTTVYDKGSEVMRMYLTILGEEYYKKGFDIYIKKNDGNTATCEDFNYAMEQAYKMKKADNSANLNQYLLWFSQSGTPHVSFKYNYDAEKKQYSIHVNQYTKPDENQKEKKPLFIPISVGLINPENGKEMISQTTLELTKESDTFVFNNIAVKPIPSLFRGFSAPVYIEDQLTDEERILLLKYDSDAFVRYNSCTNIYMKQILMNYNEFLKAKNEKLESFQLTPVNAQFIDAIKYLLEDPHADAGFKSYIVSLPQDRYIINFVSNLDTDVLADTKEYIYKQIGDKLNDVYYKMFKSLEAKADDLTYFNDESHVDFDQMNMRTLRNTLLSLLSKAQYPNILNEIIEHSKSPYPSNWLTSLSVSAYFDKYFELYDKTYKLSKDDELLLQEWLKTVSRSDRKDIYEILKKLENEVLKDSKNPNDIRAVYLPFTNNLRRFHDISGKGYKLIAEVITKTDKFNPMVATQLCEPFKLWNKLDTKRQELMLNEMNTMLQEPQISNNLKEYLLRLTNKL

Source

organism	Plasmodium falciparum
ncbi_taxonomy_id	5833
host_organism	Escherichia coli

Entity 2 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	2

Entity 3 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 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	406

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6. Citations (1)

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length_a	73.953 Å
length_b	109.530 Å
length_c	116.750 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.200 Å
resolution_low	49.580 Å
r_factor	0.1968
r_work	0.1945
r_free	0.2397

fit	/app/data/saxs_computation/y6/9y65/9y65.fit
pddf	/app/data/pr_computation/y6/9y65/9y65.pr.out
profile	/app/data/saxs_computation/y6/9y65/9y65.dat

Plasmodium falciparum M1 aminopeptidase (PfA-M1) bound to inhibitor 3k (MIPS3415)

SAXS Profile

P(r) Distribution