SAXSdb — 5ccv

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

RNA-directed RNA polymerase NS5

Dengue virus type 3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 2 S-ADENOSYL-L-HOMOCYSTEINE × 1	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 S-ADENOSYL-L-HOMOCYSTEINE × 2	Consistent with protein count
11	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 S-ADENOSYL-L-HOMOCYSTEINE × 2	Consistent with protein count
12	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 S-ADENOSYL-L-HOMOCYSTEINE × 2	Consistent with protein count
13	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 S-ADENOSYL-L-HOMOCYSTEINE × 2	Consistent with protein count
14	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 S-ADENOSYL-L-HOMOCYSTEINE × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 S-ADENOSYL-L-HOMOCYSTEINE × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 2 S-ADENOSYL-L-HOMOCYSTEINE × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 2 S-ADENOSYL-L-HOMOCYSTEINE × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ZINC ION × 2 S-ADENOSYL-L-HOMOCYSTEINE × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	ZINC ION × 2 S-ADENOSYL-L-HOMOCYSTEINE × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	ZINC ION × 2 S-ADENOSYL-L-HOMOCYSTEINE × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	ZINC ION × 2 S-ADENOSYL-L-HOMOCYSTEINE × 1	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 S-ADENOSYL-L-HOMOCYSTEINE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_DEN3P
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–894； UniProt 2491–3390 Author chain B； PDBConstruct 1–894； UniProt 2491–3390 Author chain C； PDBConstruct 1–894； UniProt 2491–3390 Author chain D； PDBConstruct 1–894； UniProt 2491–3390 Author chain E； PDBConstruct 1–894； UniProt 2491–3390 Author chain F； PDBConstruct 1–894； UniProt 2491–3390 Author chain G； PDBConstruct 1–894； UniProt 2491–3390 Author chain H； PDBConstruct 1–894； UniProt 2491–3390

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	5ccv
Deposition date deposition_date	2015-07-02
Structure title title	Crystal structure of full-length NS5 from dengue virus type 3
Keywords keywords	methyltransferase, nonstructural protein, 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.

5ccv__assembly_12__model_1

Assembly 12 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5ccv__assembly_12__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ccv__assembly_12__model_1 | P(r) · Pending

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

Rg（Guinier）	43.46 Å
Rg (electron density)	43.22 Å
Total Rg	43.45 Å
Atom count	13696
Residues	1695
Excluded volume	242630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ccv__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ccv__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5ccv__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5ccv__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5ccv__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5ccv__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`5ccv__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`5ccv__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`5ccv__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`5ccv__assembly_10__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`5ccv__assembly_11__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`5ccv__assembly_12__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`5ccv__assembly_13__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`5ccv__assembly_14__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 (3)

Entity 1 Entity 1 polymer

Description description	RNA-directed RNA polymerase NS5
Molecular weight formula_weight	104140.0 kDa
EC 编号 ec_number	2.1.1.56,2.1.1.57,2.7.7.48
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	52681

GTGSQGETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGEITHHAVSRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTVEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVRNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVDLGAGTRHVNAEPETPNMDVIGERIKRIKEEHSSTWHYDDENPYKTWAYHGSYEVKATGSASSMINGVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTPRPMPGTRKVMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTNAAMGAVFTEENQWDSARAAVEDEEFWKLVDRERELHKLGKCGSCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARYLEFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHNEEKITQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPKGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLIRQMEGEGVLSKADLENPHPLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSLRETACLGKAYAQMWALMYFHRRDLRLASNAICSAVPVHWVPTSRTTHQWMTTEDMLTVWNRVWIEDNPWMEDKTPVTTWEDVPYLGKREDQWCGSLIGLTSRATWAQNILTAIQQVRSLIGNEEFLDYMPSMKRFRKEEESEGAIWAAALEHHHHHH

Source Source

Source organism organism	Dengue virus type 3
Common name common_name	DENV-3
NCBI taxonomy ID ncbi_taxonomy_id	408870
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	16

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	8

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5ccvA01
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

Domain ID domain_id	5ccvB01
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

Domain ID domain_id	5ccvC01
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

Domain ID domain_id	5ccvD01
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

Domain ID domain_id	5ccvE01
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

Domain ID domain_id	5ccvF01
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

Domain ID domain_id	5ccvG01
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

Domain ID domain_id	5ccvH01
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	215.314 Å
Unit-cell length b length_b	215.314 Å
Unit-cell length c length_c	480.683 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	48

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	49.217 Å
R factor r_factor	0.2386
R_work r_work	0.2381
R_free r_free	0.2737

Crystal structure of full-length NS5 from dengue virus type 3

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

5ccv__assembly_12__model_1

5ccv__assembly_12__model_1 | I(q)

5ccv__assembly_12__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of full-length NS5 from dengue virus type 3

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

5ccv__assembly_12__model_1

5ccv__assembly_12__model_1 | I(q)

5ccv__assembly_12__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)