SAXSdb — 2jly

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

SERINE PROTEASE SUBUNIT NS3

DENGUE VIRUS 4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	5'-R(APGPAPCPUPAPAPCPAPAPCPU)-3' × 1 ADENOSINE-5'-DIPHOSPHATE × 1 PHOSPHATE ION × 1 MANGANESE (II) ION × 1 GLYCEROL × 1 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	5'-R(APGPAPCPUPAPAPCPAPAPCPU)-3' × 1 ADENOSINE-5'-DIPHOSPHATE × 1 PHOSPHATE ION × 1 MANGANESE (II) ION × 1 GLYCEROL × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_DEN4T
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–451； UniProt 1646–2092 Author chain B； PDBConstruct 5–451； UniProt 1646–2092

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	2jly
Deposition date deposition_date	2008-09-15
Structure title title	Dengue virus 4 NS3 helicase in complex with ssRNA and ADP-Phosphate
Keywords keywords	;HYDROLASE-RNA COMPLEX, ENVELOPE PROTEIN, RIBONUCLEOPROTEIN, CAPSID PROTEIN, RNA REPLICATION, SERINE PROTEASE, GLYCOPROTEIN, DENGUE VIRUS, METAL-BINDING, TRANSFERASE, ATP-BINDING, RNA-BINDING, FLAVIVIRUSES, TRANSCRIPTION REGULATION, RNA-DIRECTED RNA POLYMERASE, NUCLEOTIDE-BINDING, VIRAL NUCLEOPROTEIN, SECRETED, HELICASE, PROTEASE, HYDROLASE, PHOSPHATE, CLEAVAGE ON PAIR OF BASIC RESIDUES, ENDOPLASMIC RETICULUM, NUCLEOTIDYLTRANSFERASE, ADP, SSRNA, VIRION, ATPASE, NUCLEUS, MEMBRANE, TRANSMEMBRANE, TRANSCRIPTION, PHOSPHOPROTEIN, NS3 HELICASE STRUCTURE, MULTIFUNCTIONAL ENZYME ;; HYDROLASE/RNA
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.

2jly__assembly_1__model_1

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

Download this curve (.dat)

2jly__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2jly__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.60 Å
Rg (electron density)	22.71 Å
Total Rg	23.51 Å
Atom count	3788
Residues	458
Excluded volume	66549 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2jly__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2jly__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	SERINE PROTEASE SUBUNIT NS3
Molecular weight formula_weight	51337.5 kDa
EC 编号 ec_number	3.4.21.91
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	7942

GSAMGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLRRLRTLILAPTRVVAAEMEEALRGLPIRYQTPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAIFMTATPPGSTDPFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPEGIIPTLFGPEREKTQAIDGEFRLRGEQRKTFVELMRRGDLPVWLSYKVASAGISYKDREWCFTGERNNQILEENMEVEIWTREGEKKKLRPKWLDARVYADPMALKDFKEFASGRK

Source Source

Source organism organism	DENGUE VIRUS 4
NCBI taxonomy ID ncbi_taxonomy_id	408688
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	5'-R(APGPAPCPUPAPAPCPAPAPCPU)-3'
Molecular weight formula_weight	3803.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,D

AGACUAACAACU

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	380

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2jlya1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.14 — RNA helicase

Domain ID domain_id	d2jlya2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d2jlya3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2jlyb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.14 — RNA helicase

Domain ID domain_id	d2jlyb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d2jlyb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	2jlyA01
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	2jlyA02
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	2jlyB01
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	2jlyB02
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

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Unit-cell length a length_a	131.748 Å
Unit-cell length b length_b	105.591 Å
Unit-cell length c length_c	72.671 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.68 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.2019
R_work r_work	0.1991
R_free r_free	0.2549

Dengue virus 4 NS3 helicase in complex with ssRNA and ADP-Phosphate

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

SERINE PROTEASE SUBUNIT NS3

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

2jly__assembly_1__model_1

2jly__assembly_1__model_1 | I(q)

2jly__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Dengue virus 4 NS3 helicase in complex with ssRNA and ADP-Phosphate

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

SERINE PROTEASE SUBUNIT NS3

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

2jly__assembly_1__model_1

2jly__assembly_1__model_1 | I(q)

2jly__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)