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9va8

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

Method: X-RAY DIFFRACTION D_max: 57.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9va8
deposition_date	2025-06-03
last_revision	2026-05-06
title	Crystal Structure of Human Cathepsin B with a L-peptide substrate
keywords	covalent inhibitor, 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	18.20 Å
rg_electron	17.15 Å
i0	15402600.00
molecular_weight	28198.0 kDa
excluded_volume	34627 Å³
envelope_volume	38492 Å³
shell_volume	18349 Å³
envelope_diameter	58.2 Å
shell_rg	23.73 Å
envelope_rg	17.54 Å
shape_rg	17.12 Å
total_rg	18.19 Å
total_atoms	1981
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	57.3 Å
rg_real	18.09 Å
rg_real_error	0.25 Å
i0_real	1.5400e+07
i0_real_error	1.8600e+05
rg_reciprocal	18.10 Å
i0_reciprocal	15400000.0000
total_estimate	0.8936
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.2 Å
skewness	0.156
kurtosis	-0.386
angular_range	— – 0.4350 Å⁻¹
current_alpha	0.0000
highest_alpha	3499000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.986

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Cathepsin B
formula_weight	27811.0 kDa
ec_number	3.4.22.1
mutation	S115A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2189

LPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGARPPCTGEGDTPKCSKICEPGYAPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGIPRTD

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)YY(F3V)
formula_weight	425.5 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

XYYX

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	208

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6. Citations (1)

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length_a	30.617 Å
length_b	75.096 Å
length_c	97.642 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	28.370 Å
r_factor	0.1797
r_work	0.1782
r_free	0.2088

fit	/app/data/saxs_computation/va/9va8/9va8.fit
pddf	/app/data/pr_computation/va/9va8/9va8.pr.out
profile	/app/data/saxs_computation/va/9va8/9va8.dat

Crystal Structure of Human Cathepsin B with a L-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)