SAXSdb — 5yvj

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

Genome polyprotein

Dengue virus 4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （Q2YHE8） GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	F8TEL4_9FLAV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–618； UniProt 1475–2092

Genome polyprotein

Dengue virus 4

UniProt Q2YHE8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （F8TEL4） GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2YHE8_9FLAV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–47； UniProt 1393–1439

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	5yvj
Deposition date deposition_date	2017-11-26
Structure title title	Crystal structure of full length NS2B47-NS3 (gD4NS2BNS3) from Dengue virus 4 in open conformation
Keywords keywords	Serine Protease, Helicase, Non-structural protein 3, Dengue, Flavivirus, VIRAL PROTEIN; VIRAL PROTEIN
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.

5yvj__assembly_1__model_1

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

Download this curve (.dat)

5yvj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5yvj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.09 Å
Rg (electron density)	28.61 Å
Total Rg	29.15 Å
Atom count	4718
Residues	604
Excluded volume	83813 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5yvj__assembly_1__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	69501.3 kDa
Mutation mutation	S135A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	4842

SGALWDVPSPAATQKATLSEGVYRIMQRGLFGKTQVGVGIHMEGVFHTMWHVTRGSVICHETGRLEPSWADVRNDMISYGGGWRLGDKWDKEEDVQVLAIEPGKNPKHVQTKPGLFKTLTGEIGAVTLDFKPGTAGSPIINKKGKVIGLYGNGVVTKSGDYVSAITQAERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGLPIRYQTPAVKSEHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAIFMTATPPGSIDPFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKKVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPEGIIPTLFGPEREKTQAIDGEFRLRGEQRKTFVELMRRGDLPVWLSYKVASAGISYKDREWCFTGERNNQILEENMEVEIWTREGEKKKLRPKWLDARVYADPMALKDFKEFASGRK

Source Source

Source organism organism	Dengue virus 4
NCBI taxonomy ID ncbi_taxonomy_id	11070
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	5201.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

ADLSLEKAANVQWDEMADITGSSPIIEVKQDEDGSFSIRDVEETNMI

Source Source

Source organism organism	Dengue virus 4
NCBI taxonomy ID ncbi_taxonomy_id	11070
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

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Unit-cell length a length_a	52.780 Å
Unit-cell length b length_b	86.810 Å
Unit-cell length c length_c	75.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.508 Å
Low-resolution limit resolution_low	45.051 Å
R factor r_factor	0.1907
R_work r_work	0.1879
R_free r_free	0.2456

Crystal structure of full length NS2B47-NS3 (gD4NS2BNS3) from Dengue virus 4 in open conformation

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

Genome polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

Genome polyprotein

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

5yvj__assembly_1__model_1

5yvj__assembly_1__model_1 | I(q)

5yvj__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of full length NS2B47-NS3 (gD4NS2BNS3) from Dengue virus 4 in open conformation

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

Genome polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Genome polyprotein

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

5yvj__assembly_1__model_1

5yvj__assembly_1__model_1 | I(q)

5yvj__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)