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9xhr

Crystal Structure of Human Cathepsin B with a D-peptide substrate

Method: X-RAY DIFFRACTION D_max: 57.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xhr
deposition_date	2025-11-02
last_revision	2026-05-06
title	Crystal Structure of Human Cathepsin B with a D-peptide substrate
keywords	complex, D-peptide substrate, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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	18.09 Å
rg_electron	17.22 Å
i0	27838600.00
molecular_weight	26739.0 kDa
excluded_volume	25624 Å³
envelope_volume	39218 Å³
shell_volume	18585 Å³
envelope_diameter	57.3 Å
shell_rg	23.85 Å
envelope_rg	17.63 Å
shape_rg	17.19 Å
total_rg	17.96 Å
total_atoms	2011
n_residues	256
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	57.0 Å
rg_real	17.96 Å
rg_real_error	0.23 Å
i0_real	2.7840e+07
i0_real_error	2.7340e+05
rg_reciprocal	17.98 Å
i0_reciprocal	27840000.0000
total_estimate	0.8920
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.1 Å
skewness	0.174
kurtosis	-0.381
angular_range	— – 0.4400 Å⁻¹
current_alpha	0.0000
highest_alpha	5377000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.969

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Cathepsin B
formula_weight	27956.2 kDa
ec_number	3.4.22.1
mutation	S115A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2272

KLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGARPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGIPRTD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Mammalian expression vector BsrGI-MCS-pcDNA3.1

Entity 2 polymer

description	ACE-DAR-DLY-DTY-DTY-GLY-0QE
formula_weight	745.3 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(D)
strand_id	C

XRKYYGX

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	261

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6. Citations (1)

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length_a	31.098 Å
length_b	81.331 Å
length_c	94.219 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	—

resolution	1.500 Å
resolution_low	30.800 Å
r_factor	0.1479
r_work	0.1467
r_free	0.1697

fit	/app/data/saxs_computation/xh/9xhr/9xhr.fit
pddf	/app/data/pr_computation/xh/9xhr/9xhr.pr.out
profile	/app/data/saxs_computation/xh/9xhr/9xhr.dat

Crystal Structure of Human Cathepsin B with a D-peptide substrate

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

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)