SAXSdb — 4deq

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

Neuropilin-1, Vascular endothelial growth factor A

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	PHOSPHATE ION × 1 water × 2	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	PHOSPHATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NRP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–160； UniProt 274–429 Author chain B； PDBConstruct 5–160； UniProt 274–429

Neuropilin-1, Vascular endothelial growth factor A

Homo sapiens

UniProt P15692

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	PHOSPHATE ION × 1 water × 2	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	PHOSPHATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VEGFA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 169–218； UniProt 183–232 Author chain B； PDBConstruct 169–218； UniProt 183–232

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	4deq
Deposition date deposition_date	2012-01-21
Structure title title	Structure of the Neuropilin-1/VEGF-A complex
Keywords keywords	Coagulation factor domain, heparin binding domain, Angiogenesis, PROTEIN BINDING-CYTOKINE complex; PROTEIN BINDING/CYTOKINE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4deq__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4deq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4deq__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	27.34 Å
Rg (electron density)	26.35 Å
Total Rg	27.30 Å
Atom count	3429
Residues	432
Excluded volume	60452 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4deq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4deq__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4deq__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Neuropilin-1, Vascular endothelial growth factor A
Molecular weight formula_weight	24660.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3445

GSHMKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKITDYVDGSGSGSPCGPCSERRKHLFVQDPQTCKCSCKNTDSRCKARQLELNERTCRCDKPRR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4deqA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	4deqA02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	160 — Vascular Endothelial Growth Factor-165, Heparin-binding Domain
Homologous superfamily homologous superfamily	10 — Vascular endothelial growth factor, heparin-binding domain

Domain ID domain_id	4deqB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	4deqB02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	160 — Vascular Endothelial Growth Factor-165, Heparin-binding Domain
Homologous superfamily homologous superfamily	10 — Vascular endothelial growth factor, heparin-binding domain

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Unit-cell length a length_a	114.978 Å
Unit-cell length b length_b	114.978 Å
Unit-cell length c length_c	50.946 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	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.649 Å
Low-resolution limit resolution_low	19.900 Å
R factor r_factor	0.2115
R_work r_work	0.2088
R_free r_free	0.2670

Structure of the Neuropilin-1/VEGF-A complex

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

Neuropilin-1, Vascular endothelial growth factor A

State in the Current Structure

Other States of the Same Protein in the Database

Neuropilin-1, Vascular endothelial growth factor A

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4deq__assembly_1__model_1

4deq__assembly_1__model_1 | I(q)

4deq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the Neuropilin-1/VEGF-A complex

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

Neuropilin-1, Vascular endothelial growth factor A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Neuropilin-1, Vascular endothelial growth factor A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4deq__assembly_1__model_1

4deq__assembly_1__model_1 | I(q)

4deq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)