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9qwd

X-ray structure of furin (PCSK3) in complex with the biphenyl-derived compound 34 (mi2470)

Method: X-RAY DIFFRACTION D_max: 73.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qwd
deposition_date	2025-04-14
last_revision	2025-12-24
title	X-ray structure of furin (PCSK3) in complex with the biphenyl-derived compound 34 (mi2470)
keywords	furin, proprotein convertase subtilisin/kexin type 3, PCSK3, antiviral, inhibitor, protease, complex, 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	22.68 Å
rg_electron	21.70 Å
i0	49396600.00
molecular_weight	52038.0 kDa
excluded_volume	63933 Å³
envelope_volume	72578 Å³
shell_volume	27137 Å³
envelope_diameter	74.1 Å
shell_rg	29.32 Å
envelope_rg	21.97 Å
shape_rg	21.69 Å
total_rg	22.59 Å
total_atoms	7102
n_residues	472
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	73.2 Å
rg_real	22.57 Å
rg_real_error	0.40 Å
i0_real	4.9400e+07
i0_real_error	6.2880e+05
rg_reciprocal	22.60 Å
i0_reciprocal	49400000.0000
total_estimate	0.8884
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.7 Å
skewness	0.224
kurtosis	-0.363
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	10960000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.978

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Furin
formula_weight	52388.6 kDa
ec_number	3.4.21.75
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8106

DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	6

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	1-[[3-[3,5-bis(chloranyl)phenyl]-5-[(4-pyridin-4-ylpiperazin-1-yl)methyl]phenyl]methyl]-4-pyridin-4-yl-piperazine
formula_weight	573.6 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	444

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6. Citations (1)

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length_a	131.507 Å
length_b	131.507 Å
length_c	155.350 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65 2 2
int_tables_number	179
crystal_system	hexagonal

resolution	1.600 Å
resolution_low	45.930 Å
r_factor	0.1363
r_work	0.1350
r_free	0.1608

fit	/app/data/saxs_computation/qw/9qwd/9qwd.fit
pddf	/app/data/pr_computation/qw/9qwd/9qwd.pr.out
profile	/app/data/saxs_computation/qw/9qwd/9qwd.dat