SAXSdb — 3lkw

▼

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

fusion protein of nonstructural protein 2B and nonstructural protein 3

Dengue virus type 1 (strain Nauru/West Pac/1974)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	CHLORIDE ION × 2 CADMIUM ION × 2 SULFATE ION × 2 GLYCEROL × 2 water × 2	Consistent with protein count
2	Insufficient information	Homooligomer	Protein 4	CHLORIDE ION × 4 CADMIUM ION × 4 SULFATE ION × 4 GLYCEROL × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_DEN1W
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 61–236； UniProt 1476–1661

fusion protein of nonstructural protein 2B and nonstructural protein 3

Dengue virus type 1 (strain Nauru/West Pac/1974)

UniProt P33478

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	CHLORIDE ION × 2 CADMIUM ION × 2 SULFATE ION × 2 GLYCEROL × 2 water × 2	Consistent with protein count
2	Insufficient information	Homooligomer	Protein 4	CHLORIDE ION × 4 CADMIUM ION × 4 SULFATE ION × 4 GLYCEROL × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_DEN1S
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–51； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3lkw
Deposition date deposition_date	2010-01-28
Structure title title	Crystal Structure of Dengue Virus 1 NS2B/NS3 protease active site mutant
Keywords keywords	viral protease, serine protease, NS3 PROTEASE, NS2B COFACTOR, VIRAL PROTEIN, HYDROLASE; VIRAL PROTEIN,HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3lkw__assembly_1__model_1

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

Download this curve (.dat)

3lkw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lkw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.56 Å
Rg (electron density)	24.41 Å
Total Rg	25.33 Å
Atom count	3186
Residues	422
Excluded volume	56211 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lkw__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3lkw__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	fusion protein of nonstructural protein 2B and nonstructural protein 3
Molecular weight formula_weight	25046.9 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13,2.1.1.56,2.1.1.57,2.7.7.48
Mutation mutation	deletion NS3 PROTEASE, residues 1486-1495
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1694

GAHMADLSLEKAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLGGGGSGGGGSGVLWDTPSPGIYRILQRGLLGRSQVGVGVFQEGVFHTMWHVTRGAVLMYQGKRLEPSWASVKKDLISYGGGWRFQGSWNAGEEVQVIAVEPGKNPKNVQTAPGTFKTPEGEVGAIALDFKPGTAGSPIVNREGKIVGLYGNGVVTTSGTYVSAIAQAKASQEGPLPEIEDEVFRK

Source Source

Source organism organism	Dengue virus type 1 (strain Nauru/West Pac/1974)
Common name common_name	DENV-1
NCBI taxonomy ID ncbi_taxonomy_id	11059
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	88

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3lkwA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	3lkwA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

▶

Unit-cell length a length_a	56.868 Å
Unit-cell length b length_b	60.893 Å
Unit-cell length c length_c	160.616 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2070
R_work r_work	0.2050
R_free r_free	0.2490

Crystal Structure of Dengue Virus 1 NS2B/NS3 protease active site mutant

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

fusion protein of nonstructural protein 2B and nonstructural protein 3

State in the Current Structure

Other States of the Same Protein in the Database

fusion protein of nonstructural protein 2B and nonstructural protein 3

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

3lkw__assembly_1__model_1

3lkw__assembly_1__model_1 | I(q)

3lkw__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Dengue Virus 1 NS2B/NS3 protease active site mutant

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

fusion protein of nonstructural protein 2B and nonstructural protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

fusion protein of nonstructural protein 2B and nonstructural protein 3

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

3lkw__assembly_1__model_1

3lkw__assembly_1__model_1 | I(q)

3lkw__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)