SAXSdb — 5yvu

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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 3	Pancreatic trypsin inhibitor × 1 （P00974） GLYCEROL × 1 water × 3	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, 2
Chains and sequence ranges	Author chain B； PDBConstruct 10–627； UniProt 1475–2092 Author chain A； PDBConstruct 9–55； UniProt 1393–1439

Pancreatic trypsin inhibitor

Bos taurus

UniProt P00974

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Genome polyprotein × 1 （F8TEL4） Genome polyprotein × 1 （F8TEL4） GLYCEROL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BPT1_BOVIN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–55； UniProt 36–90

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	5yvu
Deposition date deposition_date	2017-11-27
Structure title title	Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain
Keywords keywords	SERINE PROTEASE, NON-STRUCTURAL PROTEIN 3, DEAH HELICASE, FLAVIVIRUS, DENGUE, 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.

5yvu__assembly_1__model_1

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

Download this curve (.dat)

5yvu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5yvu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.13 Å
Rg (electron density)	30.72 Å
Total Rg	31.25 Å
Atom count	5302
Residues	694
Excluded volume	93784 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5yvu__assembly_1__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	70044.8 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	5350

GGGGSGGGGSGALWDVPSPAATQKATLSEGVYRIMQRGLFGKTQVGVGIHMEGVFHTMWHVTRGSVICHETGRLEPSWADVRNDMISYGGGWRLGDKWDKEEDVQVLAIEPGKNPKHVQTKPGLFKTLTGEIGAVTLDFKPGTAGSPIINKKGKVIGLYGNGVVTKSGDYVSAITQAERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGLPIRYQTPAVKSEHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAIFMTATPPGSIDPFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKKVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPEGIIPTLFGPEREKTQAIDGEFRLRGEQRKTFVELMRRGDLPVWLSYKVASAGISYKDREWCFTGERNNQILEENMEVEIWTREGEKKKLRPKWLDARVYADPMALKDFKEFASGRK

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	5964.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

FKPGTSGSADLSLEKAANVQWDEMADITGSSPIIEVKQDEDGSFSIRDVEETNMI

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 polymer

Description description	Pancreatic trypsin inhibitor
Molecular weight formula_weight	6342.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTC

Source Source

Source organism organism	Bos taurus
Common name common_name	Bovine
NCBI taxonomy ID ncbi_taxonomy_id	9913
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	48

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5yvui_
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	5yvuB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5yvuB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5yvuI00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

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Unit-cell length a length_a	53.059 Å
Unit-cell length b length_b	85.627 Å
Unit-cell length c length_c	85.508 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.95 °
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	2.491 Å
Low-resolution limit resolution_low	47.704 Å
R factor r_factor	0.2241
R_work r_work	0.2219
R_free r_free	0.2659

Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain

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

Pancreatic trypsin inhibitor

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

5yvu__assembly_1__model_1

5yvu__assembly_1__model_1 | I(q)

5yvu__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain

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

Pancreatic trypsin inhibitor

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

5yvu__assembly_1__model_1

5yvu__assembly_1__model_1 | I(q)

5yvu__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)