SAXSdb — 10sb

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1. Structure Basics

entry_id	10sb
deposition_date	2026-02-04
last_revision	2026-06-03
title	PCSK9 in complex with cyclic peptide 21
keywords	CHOLESTEROL, LDL RECEPTOR, EGFA DOMAIN, 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	21.98 Å
rg_electron	21.24 Å
i0	56374600.00
molecular_weight	38705.0 kDa
excluded_volume	37188 Å³
envelope_volume	60221 Å³
shell_volume	23667 Å³
envelope_diameter	74.8 Å
shell_rg	27.96 Å
envelope_rg	21.56 Å
shape_rg	21.23 Å
total_rg	21.86 Å
total_atoms	2931
n_residues	379
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	73.7 Å
rg_real	21.93 Å
rg_real_error	0.42 Å
i0_real	5.6370e+07
i0_real_error	7.1240e+05
rg_reciprocal	21.94 Å
i0_reciprocal	56370000.0000
total_estimate	0.8797
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.4 Å
skewness	0.337
kurtosis	-0.275
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	11780000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Propeptide of Proprotein convertase subtilisin/kexin type 9
formula_weight	13791.5 kDa
ec_number	3.4.21.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3192

QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Proprotein convertase subtilisin/kexin type 9
formula_weight	32836.9 kDa
ec_number	3.4.21.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAGNSHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Cyclic peptide 21
formula_weight	1142.2 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

XAXXWPTYX

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	N-{[4-(2-aminoethyl)phenyl]methyl}hexan-1-amine
formula_weight	234.4 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	GLYCOLIC ACID
formula_weight	76.1 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	253

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6. Citations (1)

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length_a	70.741 Å
length_b	70.741 Å
length_c	159.125 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	1.828 Å
resolution_low	24.270 Å
r_factor	0.1985
r_work	0.1963
r_free	0.2385

fit	/app/data/saxs_computation/0s/10sb/10sb.fit
pddf	/app/data/pr_computation/0s/10sb/10sb.pr.out
profile	/app/data/saxs_computation/0s/10sb/10sb.dat

PCSK9 in complex with cyclic peptide 21

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

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)