SAXSdb — 9s8w

▼

1. Structure Basics

entry_id	9s8w
deposition_date	2025-08-05
last_revision	2025-09-24
title	Human heparanase in complex with neutralizing antibody A54 Fab fragment
keywords	Heparanase, Carbohydrate, Glycosaminoglycan, Hydrolase, Antibody, Fab; CARBOHYDRATE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	35.87 Å
rg_electron	35.75 Å
i0	150441000.00
molecular_weight	99993.0 kDa
excluded_volume	125630 Å³
envelope_volume	161650 Å³
shell_volume	39795 Å³
envelope_diameter	124.8 Å
shell_rg	39.78 Å
envelope_rg	35.98 Å
shape_rg	35.69 Å
total_rg	36.21 Å
total_atoms	14000
n_residues	896
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

▼

3. P(r) Analysis (GNOM)

dmax	123.0 Å
rg_real	36.18 Å
rg_real_error	1.25 Å
i0_real	1.5040e+08
i0_real_error	2.5740e+06
rg_reciprocal	35.99 Å
i0_reciprocal	150400000.0000
total_estimate	0.8298
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	33.5 Å
skewness	0.530
kurtosis	-0.401
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	29660000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.730; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.775; Smooth: 0.818

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	Heparanase
formula_weight	43464.1 kDa
ec_number	3.2.1.166
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	14031

KKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	Heparanase 8 kDa subunit
formula_weight	8273.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPAYLRFGGTKTDFLIFDPKKE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 3 polymer

description	A54 Fab heavy chain
formula_weight	23921.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QVQLQQSGAELAKPGASVRMSCKASGYTFTNYWMHWVKQRPGQGLEWIGYINPTTGYTEYNQKFKDKATLTADKSSSTAYMQLSSLTSEDSAVYYCARGGAGYDYDEDYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIV

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Mus musculus

Entity 4 polymer

description	A54 Fab light chain
formula_weight	24027.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIVLTQSPASLAVSLGQRATISCRASESVEYFGTSYMNWYQQKPGQPPKLLIYLASILESGIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQSNEDPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Mus musculus

Entity 5 branched

description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	367.3 kDa
src_method	man
entity_count	1

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	3

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	31

▶

6. Citations (1)

▶

length_a	69.738 Å
length_b	69.738 Å
length_c	429.781 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

resolution	3.490 Å
resolution_low	107.440 Å
r_factor	—
r_work	0.2197
r_free	0.3230

fit	/app/data/saxs_computation/s8/9s8w/9s8w.fit
pddf	/app/data/pr_computation/s8/9s8w/9s8w.pr.out
profile	/app/data/saxs_computation/s8/9s8w/9s8w.dat

Human heparanase in complex with neutralizing antibody A54 Fab fragment

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 branched

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)