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9s60

Structural and proteomics analysis of the mouse cathepsin B - DARPin 4m3 complex reveals determinants of species - specific binding

Method: X-RAY DIFFRACTION D_max: 90.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s60
deposition_date	2025-07-30
last_revision	2026-01-14
title	Structural and proteomics analysis of the mouse cathepsin B - DARPin 4m3 complex reveals determinants of species - specific binding
keywords	cysteine cathepsin B, mechanism of inhibition, species-specific binding, DARPin 4m3, 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	29.50 Å
rg_electron	28.73 Å
i0	135509000.00
molecular_weight	87659.0 kDa
excluded_volume	107690 Å³
envelope_volume	133040 Å³
shell_volume	38007 Å³
envelope_diameter	96.5 Å
shell_rg	36.58 Å
envelope_rg	28.50 Å
shape_rg	28.73 Å
total_rg	29.46 Å
total_atoms	11974
n_residues	824
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	90.6 Å
rg_real	29.39 Å
rg_real_error	0.64 Å
i0_real	1.3550e+08
i0_real_error	1.9680e+06
rg_reciprocal	29.44 Å
i0_reciprocal	135500000.0000
total_estimate	0.9096
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.2 Å
skewness	0.193
kurtosis	-0.545
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	26480000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.944

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Cathepsin B
formula_weight	27620.7 kDa
ec_number	3.4.22.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,A2
atom_count	14655

LPETFDAREQWSNCPTIGQIRDQGSCGSCWAFGAVEAISDRTCIHTNGRVNVEVSAEDLLTCCGIQCGDGCNGGYPSGAWSFWTKKGLVSGGVYNSHVGCLPYTIPPCEHHVNGSRPPCTGEGDTPRCNKSCEAGYSPSYKEDKHFGYTSYSVSNSVKEIMAEIYKNGPVEGAFTVFSDFLTYKSGVYKHEAGDMMGGHAIRILGWGVENGVPYWLAANSWNLDWGDNGFFKILRGENHCGIESEIVAGIPRTD

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 polymer

description	DARPin 4m3
formula_weight	18450.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,B2

MDLGKKLLDAASAGQDDEVRILMANGADVNASDAHGRTPLHAAAWSGHLEIVDVLLAHGADVNASDKYGYTPLHLAASYGHLEIVDVLLANGADVNASSKYGNTPLHVAATSGHLEIVDVLLAHGADVNANTAAGKTPFDLAIDNGNEDIAEVLQKAAAAALEVLFQGPLEHHHHHH

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	880

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6. Citations (1)

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length_a	52.640 Å
length_b	109.920 Å
length_c	142.640 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.690 Å
resolution_low	49.390 Å
r_factor	0.1931
r_work	0.1931
r_free	0.2161

fit	/app/data/saxs_computation/s6/9s60/9s60.fit
pddf	/app/data/pr_computation/s6/9s60/9s60.pr.out
profile	/app/data/saxs_computation/s6/9s60/9s60.dat

Structural and proteomics analysis of the mouse cathepsin B - DARPin 4m3 complex reveals determinants of species - specific binding

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)