SAXSdb — 3hky

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

RNA-directed RNA polymerase

Hepatitis C virus subtype 1b

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;(11S)-10-[(2,5-dimethyl-1,3-oxazol-4-yl)carbonyl]-11-{2-fluoro-4-[(2-methylprop-2-en-1-yl)oxy]phenyl}-3,3-dimethyl-2,3,4,5,10,11-hexahydrothiopyrano[3,2-b][1,5]benzodiazepin-6-ol 1,1-dioxide ; × 1 SULFATE ION × 6 CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;(11S)-10-[(2,5-dimethyl-1,3-oxazol-4-yl)carbonyl]-11-{2-fluoro-4-[(2-methylprop-2-en-1-yl)oxy]phenyl}-3,3-dimethyl-2,3,4,5,10,11-hexahydrothiopyrano[3,2-b][1,5]benzodiazepin-6-ol 1,1-dioxide ; × 1 SULFATE ION × 2 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_HCVJ4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–573； UniProt 2420–2989 Author chain B； PDBConstruct 4–573； UniProt 2420–2989

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	3hky
Deposition date deposition_date	2009-05-26
Structure title title	HCV NS5B polymerase genotype 1b in complex with 1,5 benzodiazepine 6
Keywords keywords	HEPATITIS C VIRUS, 1, 5-BENZODIAZEPINE, genotype, NS5B, polymerase, Biacore, replicon, 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.

3hky__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3hky__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hky__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.08 Å
Rg (electron density)	23.96 Å
Total Rg	24.86 Å
Atom count	4414
Residues	560
Excluded volume	78596 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hky__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3hky__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	RNA-directed RNA polymerase
Molecular weight formula_weight	64817.3 kDa
EC 编号 ec_number	2.7.7.48
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	9585

MASSMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHSLSRARPRLEHHHHHH

Source Source

Source organism organism	Hepatitis C virus subtype 1b
NCBI taxonomy ID ncbi_taxonomy_id	31647
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;(11S)-10-[(2,5-dimethyl-1,3-oxazol-4-yl)carbonyl]-11-{2-fluoro-4-[(2-methylprop-2-en-1-yl)oxy]phenyl}-3,3-dimethyl-2,3,4,5,10,11-hexahydrothiopyrano[3,2-b][1,5]benzodiazepin-6-ol 1,1-dioxide ;
Molecular weight formula_weight	581.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	672

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3hkya1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.4 — RNA-dependent RNA-polymerase

Domain ID domain_id	d3hkya2
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	d3hkyb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.4 — RNA-dependent RNA-polymerase

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Unit-cell length a length_a	106.274 Å
Unit-cell length b length_b	107.679 Å
Unit-cell length c length_c	133.573 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	44.900 Å
R factor r_factor	0.1842
R_work r_work	0.1840
R_free r_free	0.2086

HCV NS5B polymerase genotype 1b in complex with 1,5 benzodiazepine 6

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

RNA-directed RNA polymerase

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

3hky__assembly_2__model_1

3hky__assembly_2__model_1 | I(q)

3hky__assembly_2__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)

HCV NS5B polymerase genotype 1b in complex with 1,5 benzodiazepine 6

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

RNA-directed RNA polymerase

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

3hky__assembly_2__model_1

3hky__assembly_2__model_1 | I(q)

3hky__assembly_2__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)