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9rxi

Schistosoma mansoni Cathepsin D1 bound to Nb10C9

Method: X-RAY DIFFRACTION D_max: 129.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rxi
deposition_date	2025-07-11
title	Schistosoma mansoni Cathepsin D1 bound to Nb10C9
keywords	Aspartyl Protease, Schistosoma, Cathepsin, single-domain antibody, VHH, 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	42.97 Å
rg_electron	42.30 Å
i0	489129000.00
molecular_weight	188780.0 kDa
excluded_volume	238820 Å³
envelope_volume	324260 Å³
shell_volume	62802 Å³
envelope_diameter	132.6 Å
shell_rg	49.18 Å
envelope_rg	40.74 Å
shape_rg	42.30 Å
total_rg	42.66 Å
total_atoms	13277
n_residues	1732
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	129.9 Å
rg_real	42.76 Å
rg_real_error	0.74 Å
i0_real	4.8910e+08
i0_real_error	8.3890e+06
rg_reciprocal	42.97 Å
i0_reciprocal	489200000.0000
total_estimate	0.8370
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.7 Å
skewness	0.024
kurtosis	-0.641
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0001
highest_alpha	45590000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Cathepsin D (A01 family)
formula_weight	41945.0 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	13335

ETGVVRIPLHPLKSAQRTLIEFETSLEIVKKVWLSRVSGVDPQPEYLKNYLDAQYYGDITIGTPPQTFSVVFDTGSSNLWVPSKYCSYFDIACLLHRKYDSSKSSTYIPNGTEFSVHYGTGSLSGFLSTDSLQLGSLSVKGQTFGEATQQPGLVFVMAKFDGILGMAYPSISVDGVTPVFVNMIQQGIVESPVFSFYLSRNISAVLGGELMIGGIDKKYYSGEINYVDLTEQSYWLFKMDKLTISDMTACPDGCLAIADTGTSMIAGPTDEIQKINAKLGATRLPGGIYTVSCGNINNLPTIDFVINGKAMTLEPTDYLLKVSKMGSEICLTGFMGLDLPKRKLWILGDIFIGKFYTVFDMGKNRVGFAKALHPKHHHHHH

Source

organism	Schistosoma mansoni
ncbi_taxonomy_id	6183
host_organism	Homo sapiens

Entity 2 polymer

description	Nb_10C9
formula_weight	16686.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,E

QVQLQESGGGLVQAGGSLRLSCAASGRTFSTYAMGWFRQAPGKERELLAAISWSGESTYYANSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAARYVGEGPRSELLYSDLMTVDYWGLGTQVTVSSGGQHHHHHHGAEQKLISEEDLS

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	53

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6. Citations (1)

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length_a	70.141 Å
length_b	181.800 Å
length_c	78.854 Å
angle_alpha	90.00 °
angle_beta	92.41 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.590 Å
resolution_low	90.900 Å
r_factor	0.1750
r_work	0.1730
r_free	0.2341

fit	/app/data/saxs_computation/rx/9rxi/9rxi.fit
pddf	/app/data/pr_computation/rx/9rxi/9rxi.pr.out
profile	/app/data/saxs_computation/rx/9rxi/9rxi.dat

Schistosoma mansoni Cathepsin D1 bound to Nb10C9

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)