SAXSdb — 9pyf

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1. Structure Basics

entry_id	9pyf
deposition_date	2025-08-07
last_revision	2025-08-27
title	uPA Inhibitory Fab AB2 Complex
keywords	inhibitory antibody, serine protease, urokinase plasminogen activator, site directed, PROTEIN BINDING; PROTEIN BINDING
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	37.87 Å
rg_electron	37.10 Å
i0	208540000.00
molecular_weight	107830.0 kDa
excluded_volume	131190 Å³
envelope_volume	194290 Å³
shell_volume	45733 Å³
envelope_diameter	132.6 Å
shell_rg	40.95 Å
envelope_rg	37.15 Å
shape_rg	37.14 Å
total_rg	37.21 Å
total_atoms	7600
n_residues	1086
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	131.6 Å
rg_real	38.09 Å
rg_real_error	1.26 Å
i0_real	2.0850e+08
i0_real_error	3.6640e+06
rg_reciprocal	37.96 Å
i0_reciprocal	208500000.0000
total_estimate	0.8597
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	43.9 Å
skewness	0.495
kurtosis	-0.196
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	23400000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.865

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	AB2 Fab Light Chain
formula_weight	23666.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,I
atom_count	7644

EIVLTQSPLSLPVTPGEPASISCRSSQLMNRNGNNFLDWYLQKPGQSPQLLIYLGSNRAPGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMARVEAPYSFGQGTKLEIRTVVAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Urokinase-type plasminogen activator
formula_weight	32114.6 kDa
ec_number	3.4.21.73
mutation	C122A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MRGSHHHHHHGSACKPSSPPEELKFQCGQKTLRPRFKIIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli K-12

Entity 3 polymer

description	AB2 Fab Heavy Chain
formula_weight	22459.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

QLTQSGGGLVKPGRSLRLSCTASGFTFGDYAMSWVRQAPGKGLEWVGFVRSESAGATTEYAASVKGRFTISRDDSKSIAYLQMNALKTEDTAVYYCIRGANWNWGQGTLVTVSSASTKGPSVFPLAPSSKTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	44

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6. Citations (1)

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length_a	86.745 Å
length_b	86.745 Å
length_c	172.420 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43
int_tables_number	78
crystal_system	—

resolution	2.900 Å
resolution_low	86.745 Å
r_factor	0.2313
r_work	0.2278
r_free	0.2998

fit	/app/data/saxs_computation/py/9pyf/9pyf.fit
pddf	/app/data/pr_computation/py/9pyf/9pyf.pr.out
profile	/app/data/saxs_computation/py/9pyf/9pyf.dat

uPA Inhibitory Fab AB2 Complex

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)