SAXSdb — 3evg

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

RNA-directed RNA polymerase NS5

Dengue virus 2 16681-PDK53

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 5 S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_DEN27
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–266； UniProt 2493–2757

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	3evg
Deposition date deposition_date	2008-10-13
Structure title title	Crystal structure of Dengue-2 virus methyltransferase complexed with S-adenosyl-L-homocysteine
Keywords keywords	;Dengue virus, Flavivirus, NS5 Methyltransferase, RNA cap binding, ATP-binding, Capsid protein, Cleavage on pair of basic residues, Endoplasmic reticulum, Envelope protein, Glycoprotein, Helicase, Hydrolase, Membrane, Metal-binding, Multifunctional enzyme, Nucleotide-binding, Nucleotidyltransferase, Nucleus, Phosphoprotein, Protease, Ribonucleoprotein, RNA replication, RNA-binding, RNA-directed RNA polymerase, Secreted, Serine protease, Transcription, Transcription regulation, Transmembrane, Viral nucleoprotein, Virion, TRANSFERASE ;; TRANSFERASE
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.

3evg__assembly_1__model_1

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

Download this curve (.dat)

3evg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3evg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.09 Å
Rg (electron density)	18.09 Å
Total Rg	18.99 Å
Atom count	2074
Residues	257
Excluded volume	36624 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3evg__assembly_1__model_1`	monomeric （1）	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	RNA-directed RNA polymerase NS5
Molecular weight formula_weight	30836.2 kDa
EC 编号 ec_number	2.1.1.56, 2.7.7.48
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	2133

MTGNIGETLGEKWKSRLNALGKSEFQIYKKSGIQEVDRTLAKEGIKRGETDHHAVSRGSAKLRWFVERNMVTPEGKVVDLGCGRGGWSYYCGGLKNVREVKGLTKGGPGHEEPIPMSTYGWNLVRLQSGVDVFFIPPEKCDTLLCDIGESSPNPTVEAGRTLRVLNLVENWLNNNTQFCIKVLNPYMPSVIEKMEALQRKYGGALVRNPLSRNSTHEMYWVSNASGNIVSSVNMISRMLINRFTMRYKKATYEPDVDLGSGTRNIGSSSHHHHHH

Source Source

Source organism organism	Dengue virus 2 16681-PDK53
NCBI taxonomy ID ncbi_taxonomy_id	31635
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 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	59

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3evga_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.25 — mRNA cap methylase

CATH v4.4 (1 domains)

Domain ID domain_id	3evgA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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Unit-cell length a length_a	112.615 Å
Unit-cell length b length_b	112.615 Å
Unit-cell length c length_c	55.696 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	27.000 Å
R factor r_factor	0.2400
R_work r_work	0.2400
R_free r_free	0.2530

Crystal structure of Dengue-2 virus methyltransferase complexed with S-adenosyl-L-homocysteine

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

RNA-directed RNA polymerase NS5

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

3evg__assembly_1__model_1

3evg__assembly_1__model_1 | I(q)

3evg__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of Dengue-2 virus methyltransferase complexed with S-adenosyl-L-homocysteine

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

RNA-directed RNA polymerase NS5

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

3evg__assembly_1__model_1

3evg__assembly_1__model_1 | I(q)

3evg__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)