SAXSdb — 10rj

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neuropilin-1

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 其他Polymer 4 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain E； UniProt 22–855 Chain F； UniProt 22–855 Chain K； UniProt 22–855 Chain L； UniProt 22–855	Not recorded	Isoform VEGF-1 of Vascular endothelial growth factor A, long form × 4 （Q00731） Vascular endothelial growth factor receptor 2 × 4 （P35918） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;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-(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-(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-(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-(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-(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-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ; × 2 CALCIUM ION × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 3.34 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 10RJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10RI Dimeric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 22–855（834 aa） Chain F 22–855（834 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.60 Å
10RK Heparin-induced trans tetrameric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03	Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain E 22–855（834 aa） Chain F 22–855（834 aa） Chain K 22–855（834 aa） Chain L 22–855（834 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.65 Å
4GZ9 Mouse Neuropilin-1, extracellular domains 1-4 (a1a2b1b2) Deposited 2012-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–586（565 aa） Fragment：UNP RESIDUES 22-586	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 2 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES, pH 7.5, 1.5M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.223
4GZ9 Mouse Neuropilin-1, extracellular domains 1-4 (a1a2b1b2) Deposited 2012-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–586（565 aa） Fragment：UNP RESIDUES 22-586	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 4 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES, pH 7.5, 1.5M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.223
4GZA Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1 Deposited 2012-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain H 22–586（565 aa） Fragment：UNP RESIDUES 22-586	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 1% v/v ethyl acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 8% v/v acetonitrile , VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 7.00 Å R-free 0.285
7M0R Cryo-EM structure of the Sema3A/PlexinA4/Neuropilin 1 complex Deposited 2021-03-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 22–588（567 aa） Chain F 22–588（567 aa）	Not recorded	CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NRP1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 4–837； UniProt 22–855 Author chain F； PDBConstruct 4–837； UniProt 22–855 Author chain K； PDBConstruct 4–837； UniProt 22–855 Author chain L； PDBConstruct 4–837； UniProt 22–855

Isoform VEGF-1 of Vascular endothelial growth factor A, long form

Mus musculus

UniProt Q00731

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 其他Polymer 4 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 27–190 Chain B； UniProt 27–190 Chain G； UniProt 27–190 Chain H； UniProt 27–190	Not recorded	Neuropilin-1 × 4 （P97333） Vascular endothelial growth factor receptor 2 × 4 （P35918） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;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-(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-(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-(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-(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-(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-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ; × 2 CALCIUM ION × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 3.34 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 10RJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10RI Dimeric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 27–190（164 aa） Chain B 27–190（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.60 Å
10RK Heparin-induced trans tetrameric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03	Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 27–190（164 aa） Chain B 27–190（164 aa） Chain G 27–190（164 aa） Chain H 27–190（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.65 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VEGFA_MOUSE
Isoform	Q00731-2
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 12–175； UniProt 27–190 Author chain B； PDBConstruct 12–175； UniProt 27–190 Author chain G； PDBConstruct 12–175； UniProt 27–190 Author chain H； PDBConstruct 12–175； UniProt 27–190

Vascular endothelial growth factor receptor 2

Mus musculus

UniProt P35918

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 其他Polymer 4 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain C； UniProt 20–760 Chain D； UniProt 20–760 Chain I； UniProt 20–760 Chain J； UniProt 20–760	Not recorded	Neuropilin-1 × 4 （P97333） Isoform VEGF-1 of Vascular endothelial growth factor A, long form × 4 （Q00731） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;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-(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-(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-(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-(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-(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-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ; × 2 CALCIUM ION × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 3.34 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 10RJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10RI Dimeric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 20–760（741 aa） Chain D 20–760（741 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.60 Å
10RK Heparin-induced trans tetrameric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03	Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C 20–760（741 aa） Chain D 20–760（741 aa） Chain I 20–760（741 aa） Chain J 20–760（741 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.65 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VGFR2_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–744； UniProt 20–760 Author chain D； PDBConstruct 4–744； UniProt 20–760 Author chain I； PDBConstruct 4–744； UniProt 20–760 Author chain J； PDBConstruct 4–744； UniProt 20–760

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	10rj
Deposition date deposition_date	2026-02-03
Structure title title	Heparin-induced cis tetrameric complex of VEGF, VEGFR2 and Neuropilin 1
Keywords keywords	VEGF, VEGFR, neuropilin, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	87.96 Å
Radius of gyration Rg (electron density) rg_electron	89.17 Å
Forward intensity I(0) i0	5412620000.00
Molecular weight molecular_weight	604290.0 kDa
Excluded volume excluded_volume	748280 Å³
Envelope volume envelope_volume	1532000 Å³
Hydration-shell volume shell_volume	155290 Å³
Envelope diameter envelope_diameter	294.4 Å
Shell Rg shell_rg	73.25 Å
Envelope Rg envelope_rg	85.74 Å
Shape Rg shape_rg	89.25 Å
Total Rg total_rg	88.65 Å
Total atoms total_atoms	83098
Residues n_residues	5198
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	239.8 Å
Rg (real space) rg_real	84.72 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	5.1860e+09
I(0) uncertainty (real space) i0_real_error	9.8360e+07
Rg (reciprocal space) rg_reciprocal	85.78 Å
I(0) (reciprocal space) i0_reciprocal	5376000000.0000
Solution quality estimate total_estimate	0.9097
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	79.9 Å
Skewness Skewness skewness	0.334
Kurtosis Kurtosis kurtosis	-0.598
Angular range angular_range	— – 0.0900 Å⁻¹
Current regularization parameter α current_alpha	1.1540
Highest regularization parameter α highest_alpha	376500000.0000
Real-space data points n_real_points	19
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.981; Stabil: 0.970; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.005

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Neuropilin-1
Molecular weight formula_weight	95312.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,L,E,K
Atom count atom_count	83098

ELEFRSDKCGGTIKIENPGYLTSPGYPHSYHPSEKCEWLIQAPEPYQRIMINFNPHFDLEDRDCKYDYVEVIDGENEGGRLWGKFCGKIAPSPVVSSGPFLFIKFVSDYETHGAGFSIRYEIFKRGPECSQNYTAPTGVIKSPGFPEKYPNSLECTYIIFAPKMSEIILEFESFDLEQDSNPPGGMFCRYDRLEIWDGFPEVGPHIGRYCGQKTPGRIRSSSGVLSMVFYTDSAIAKEGFSANYSVLQSSISEDFKCMEALGMESGEIHSDQITASSQYGTNWSVERSRLNYPENGWTPGEDSYKEWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYRVDISSNGEDWISLKEGNKAIIFQGNTNPTDVVLGVFSKPLITRFVRIKPVSWETGISMRFEVYGCKITDYPCSGMLGMVSGLISDSQITASNQADRNWMPENIRLVTSRTGWALPPSPHPYTNEWLQVDLGDEKIVRGVIIQGGKHRENKVFMRKFKIAYSNNGSDWKTIMDDSKRKAKSFEGNNNYDTPELRTFSPLSTRFIRIYPERATHSGLGLRMELLGCEVEAPTAGPTTPNGNPVDECDDDQANCHSGTGDDFQLTGGTTVLATEKPTIIDSTIQSEFPTYGFNCEFGWGSHKTFCHWEHDSHAQLRWSVLTSKTGPIQDHTGDGNFIYSQADENQKGKVARLVSPVVYSQSSAHCMTFWYHMSGSHVGTLRVKLRYQKPEEYDQLVWMVVGHQGDHWKEGRVLLHKSLKLYQVIFEGEIGKGNLGGIAVDDISINNHISQEDCAKPTDLDKKNTEIKIDETGSTPGYEGEGEGDKNISRKPGNVLKTLDGTHHHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Isoform VEGF-1 of Vascular endothelial growth factor A, long form
Molecular weight formula_weight	20787.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,G,H

ELEHHHHHHHHAPTTEGEQKSHEVIKFMDVYQRSYCRPIETLVDIFQEYPDEIEYIFKPSCVPLMRCAGCCNDEALECVPTSESNITMQIMRIKPHQSQHIGEMSFLQHSRCECRPKKDRTKPENHCEPCSERRKHLFVQDPQTCKCSCKNTDSRCKARQLELNERTCRCDKPRR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Vascular endothelial growth factor receptor 2
Molecular weight formula_weight	84499.0 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,I,J

ELEASVGLPGDFLHPPKLSTQKDILTILANTTLQITCRGQRDLDWLWPNAQRDSEERVLVTECGGGDSIFCKTLTIPRVVGNDTGAYKCSYRDVDIASTVYVYVRDYRSPFIASVSDQHGIVYITENKNKTVVIPCRGSISNLNVSLCARYPEKRFVPDGNRISWDSEIGFTLPSYMISYAGMVFCEAKINDETYQSIMYIVVVVGYRIYDVILSPPHEIELSAGEKLVLNCTARTELNVGLDFTWHSPPSKSHHKKIVNRDVKPFPGTVAKMFLSTLTIESVTKSDQGEYTCVASSGRMIKRNRTFVRVHTKPFIAFGSGMKSLVEATVGSQVRIPVKYLSYPAPDIKWYRNGRPIESNYTMIVGDELTIMEVTERDAGNYTVILTNPISMEKQSHMVSLVVNVPPQIGEKALISPMDSYQYGTMQTLTCTVYANPPLHHIQWYWQLEEACSYRPGQTSPYACKEWRHVEDFQGGNKIEVTKNQYALIEGKNKTVSTLVIQAANVSALYKCEAINKAGRGERVISFHVIRGPEITVQPAAQPTEQESVSLLCTADRNTFENLTWYKLGSQATSVHMGESLTPVCKNLDALWKLNGTMFSNSTNDILIVAFQNASLQDQGDYVCSAQDKKTKKRHCLVKQLIILERMAPMITGNLENQTTTIGETIEVTCPASGNPTPHITWFKDNETLVEDSGIVLRDGNRNLTIRRVRKEDGGLYTCQACNVLGCARAETLFIIEGAQEKTNGTHHHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 branched

Description 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-(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-(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-(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-(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-(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-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ;
Molecular weight formula_weight	8102.6 kDa
Source method src_method	man
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	12

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.340 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.34 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	105039

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

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Neuropilin-1

State in the Current Structure

Other States of the Same Protein in the Database

Isoform VEGF-1 of Vascular endothelial growth factor A, long form

State in the Current Structure

Other States of the Same Protein in the Database

Vascular endothelial growth factor receptor 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)