SAXSdb — 5yw1

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

Peptidase S7

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	FLAVIVIRUS_NS2B × 1 （W0LLP9） PTI protein × 1 （A6QPK7） water × 1	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

FLAVIVIRUS_NS2B

Dengue virus 4

UniProt W0LLP9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Peptidase S7 × 1 （F8TEL4） PTI protein × 1 （A6QPK7） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	W0LLP9_9FLAV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 2–48； UniProt 1393–1439

PTI protein

Bos taurus

UniProt A6QPK7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Peptidase S7 × 1 （F8TEL4） FLAVIVIRUS_NS2B × 1 （W0LLP9） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A6QPK7_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	5yw1
Deposition date deposition_date	2017-11-28
Structure title title	Crystal structure of full length NS3 protein (eD4NS2BNS3) in complex with Bovine Pancreatic Trypsin Inhibitor
Keywords keywords	SERINE PROTEASE, NON-STRUCTURAL PROTEIN 3, DEAH HELICASE, ATPASE, DENGUE VIRUS, 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.

5yw1__assembly_1__model_1

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

Download this curve (.dat)

5yw1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5yw1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.20 Å
Rg (electron density)	30.77 Å
Total Rg	31.31 Å
Atom count	5275
Residues	693
Excluded volume	93208 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5yw1__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 (4)

Entity 1 Entity 1 polymer

Description description	Peptidase S7
Molecular weight formula_weight	69517.3 kDa
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	5277

SGALWDVPSPAATQKATLSEGVYRIMQRGLFGKTQVGVGIHMEGVFHTMWHVTRGSVICHETGRLEPSWADVRNDMISYGGGWRLGDKWDKEEDVQVLAIEPGKNPKHVQTKPGLFKTLTGEIGAVTLDFKPGTSGSPIINKKGKVIGLYGNGVVTKSGDYVSAITQAERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGLPIRYQTPAVKSEHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAIFMTATPPGSIDPFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKKVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPEGIIPTLFGPEREKTQAIDGEFRLRGEQRKTFVELMRRGDLPVWLSYKVASAGISYKDREWCFTGERNNQILEENMEVEIWTREGEKKKLRPKWLDARVYADPMALKDFKEFASGRK

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	FLAVIVIRUS_NS2B
Molecular weight formula_weight	5930.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

GADLSLEKAANVQWDEMADITGSSPIIEVKQDEDGSFSIRDVEETNMIGVKTQR

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	PTI protein
Molecular weight formula_weight	6372.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

RPDFCLEPPYTGPCKARMIRYFYNAKAGLCQPFVYGGCRAKRNNFKSSEDCMRTC

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5yw1i_
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	5yw1B01
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	5yw1B02
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	5yw1I00
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	53.018 Å
Unit-cell length b length_b	87.493 Å
Unit-cell length c length_c	86.455 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.25 °
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	2.600 Å
Low-resolution limit resolution_low	44.998 Å
R factor r_factor	0.2215
R_work r_work	0.2205
R_free r_free	0.2402

Crystal structure of full length NS3 protein (eD4NS2BNS3) in complex with Bovine Pancreatic Trypsin Inhibitor

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

Peptidase S7

State in the Current Structure

Other States of the Same Protein in the Database

FLAVIVIRUS_NS2B

State in the Current Structure

Other States of the Same Protein in the Database

PTI protein

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

5yw1__assembly_1__model_1

5yw1__assembly_1__model_1 | I(q)

5yw1__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of full length NS3 protein (eD4NS2BNS3) in complex with Bovine Pancreatic Trypsin Inhibitor

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

Peptidase S7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

FLAVIVIRUS_NS2B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PTI protein

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

5yw1__assembly_1__model_1

5yw1__assembly_1__model_1 | I(q)

5yw1__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)