SAXSdb — 10rk

▼

1. Structure Basics

entry_id	10rk
deposition_date	2026-02-03
title	Heparin-induced trans tetrameric complex of VEGF, VEGFR2 and Neuropilin 1
keywords	VEGF, VEGFR, neuropilin, heparin, SIGNALING PROTEIN; SIGNALING PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	85.24 Å
rg_electron	86.50 Å
i0	5034010000.00
molecular_weight	591070.0 kDa
excluded_volume	735710 Å³
envelope_volume	1428800 Å³
shell_volume	153240 Å³
envelope_diameter	358.3 Å
shell_rg	71.47 Å
envelope_rg	84.94 Å
shape_rg	86.52 Å
total_rg	86.17 Å
total_atoms	81918
n_residues	5196
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	225.8 Å
rg_real	79.24 Å
rg_real_error	0.80 Å
i0_real	4.7870e+09
i0_real_error	8.9810e+07
rg_reciprocal	82.42 Å
i0_reciprocal	4993000000.0000
total_estimate	0.9198
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	87.8 Å
skewness	0.309
kurtosis	-0.472
angular_range	— – 0.0900 Å⁻¹
current_alpha	0.6153
highest_alpha	290600000.0000
n_real_points	19
gnom_version	4.1.3
quality_criteria	AN1: 0.003; Oscil: 0.997; Stabil: 0.985; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.017

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	Neuropilin-1
formula_weight	95312.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	E,K,F,L
atom_count	81918

ELEFRSDKCGGTIKIENPGYLTSPGYPHSYHPSEKCEWLIQAPEPYQRIMINFNPHFDLEDRDCKYDYVEVIDGENEGGRLWGKFCGKIAPSPVVSSGPFLFIKFVSDYETHGAGFSIRYEIFKRGPECSQNYTAPTGVIKSPGFPEKYPNSLECTYIIFAPKMSEIILEFESFDLEQDSNPPGGMFCRYDRLEIWDGFPEVGPHIGRYCGQKTPGRIRSSSGVLSMVFYTDSAIAKEGFSANYSVLQSSISEDFKCMEALGMESGEIHSDQITASSQYGTNWSVERSRLNYPENGWTPGEDSYKEWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYRVDISSNGEDWISLKEGNKAIIFQGNTNPTDVVLGVFSKPLITRFVRIKPVSWETGISMRFEVYGCKITDYPCSGMLGMVSGLISDSQITASNQADRNWMPENIRLVTSRTGWALPPSPHPYTNEWLQVDLGDEKIVRGVIIQGGKHRENKVFMRKFKIAYSNNGSDWKTIMDDSKRKAKSFEGNNNYDTPELRTFSPLSTRFIRIYPERATHSGLGLRMELLGCEVEAPTAGPTTPNGNPVDECDDDQANCHSGTGDDFQLTGGTTVLATEKPTIIDSTIQSEFPTYGFNCEFGWGSHKTFCHWEHDSHAQLRWSVLTSKTGPIQDHTGDGNFIYSQADENQKGKVARLVSPVVYSQSSAHCMTFWYHMSGSHVGTLRVKLRYQKPEEYDQLVWMVVGHQGDHWKEGRVLLHKSLKLYQVIFEGEIGKGNLGGIAVDDISINNHISQEDCAKPTDLDKKNTEIKIDETGSTPGYEGEGEGDKNISRKPGNVLKTLDGTHHHHHHHH

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 polymer

description	Isoform VEGF-1 of Vascular endothelial growth factor A, long form
formula_weight	20787.7 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,G,H

ELEHHHHHHHHAPTTEGEQKSHEVIKFMDVYQRSYCRPIETLVDIFQEYPDEIEYIFKPSCVPLMRCAGCCNDEALECVPTSESNITMQIMRIKPHQSQHIGEMSFLQHSRCECRPKKDRTKPENHCEPCSERRKHLFVQDPQTCKCSCKNTDSRCKARQLELNERTCRCDKPRR

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	Vascular endothelial growth factor receptor 2
formula_weight	84499.0 kDa
ec_number	2.7.10.1
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,D,I,J

ELEASVGLPGDFLHPPKLSTQKDILTILANTTLQITCRGQRDLDWLWPNAQRDSEERVLVTECGGGDSIFCKTLTIPRVVGNDTGAYKCSYRDVDIASTVYVYVRDYRSPFIASVSDQHGIVYITENKNKTVVIPCRGSISNLNVSLCARYPEKRFVPDGNRISWDSEIGFTLPSYMISYAGMVFCEAKINDETYQSIMYIVVVVGYRIYDVILSPPHEIELSAGEKLVLNCTARTELNVGLDFTWHSPPSKSHHKKIVNRDVKPFPGTVAKMFLSTLTIESVTKSDQGEYTCVASSGRMIKRNRTFVRVHTKPFIAFGSGMKSLVEATVGSQVRIPVKYLSYPAPDIKWYRNGRPIESNYTMIVGDELTIMEVTERDAGNYTVILTNPISMEKQSHMVSLVVNVPPQIGEKALISPMDSYQYGTMQTLTCTVYANPPLHHIQWYWQLEEACSYRPGQTSPYACKEWRHVEDFQGGNKIEVTKNQYALIEGKNKTVSTLVIQAANVSALYKCEAINKAGRGERVISFHVIRGPEITVQPAAQPTEQESVSLLCTADRNTFENLTWYKLGSQATSVHMGESLTPVCKNLDALWKLNGTMFSNSTNDILIVAFQNASLQDQGDYVCSAQDKKTKKRHCLVKQLIILERMAPMITGNLENQTTTIGETIEVTCPASGNPTPHITWFKDNETLVEDSGIVLRDGNRNLTIRRVRKEDGGLYTCQACNVLGCARAETLFIIEGAQEKTNGTHHHHHHHH

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

Entity 5 branched

description	;2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ;
formula_weight	1750.4 kDa
src_method	man
entity_count	2

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	12

Entity 7 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	8

▶

6. Citations (1)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.650 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.65 Å
resolution_method	—
num_particles	75176

fit	/app/data/saxs_computation/0r/10rk/10rk.fit
pddf	/app/data/pr_computation/0r/10rk/10rk.pr.out
profile	/app/data/saxs_computation/0r/10rk/10rk.dat

Heparin-induced trans tetrameric complex of VEGF, VEGFR2 and Neuropilin 1

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

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 branched

Entity 6 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)