SAXSdb — 3lkh

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

RNA-directed RNA polymerase

Hepatitis C virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-(2-{[(1S)-1-benzyl-2-hydroxyethyl]amino}-2-oxoethoxy)-N-butyl-6-fluoro-N-methylbenzamide × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-(2-{[(1S)-1-benzyl-2-hydroxyethyl]amino}-2-oxoethoxy)-N-butyl-6-fluoro-N-methylbenzamide × 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 1–570； UniProt 2420–2989 Author chain B； PDBConstruct 1–570； 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	3lkh
Deposition date deposition_date	2010-01-27
Structure title title	Inhibitors of Hepatitis C Virus Polymerase: Synthesis and Characterization of Novel 6-Fluoro-N-[2-Hydroxy-1(S)-Benzamides
Keywords keywords	;HCV, NS5B, POLYMERASE, Acetylation, Apoptosis, ATP-binding, Capsid protein, Envelope protein, Fusion protein, Glycoprotein, Helicase, Host cell membrane, Host cytoplasm, Host endoplasmic reticulum, Host lipid droplet, Host membrane, Host mitochondrion, Host nucleus, Host-virus interaction, Hydrolase, Interferon antiviral system evasion, Lipoprotein, Membrane, Metal-binding, Multifunctional enzyme, Nucleotide-binding, Nucleotidyltransferase, Oncogene, Palmitate, Phosphoprotein, Protease, Ribonucleoprotein, RNA replication, RNA-binding, RNA-directed RNA polymerase, Secreted, Serine protease, SH3-binding, Thiol protease, Transcription, Transcription regulation, Transferase, Transmembrane, Ubl conjugation, Viral nucleoprotein, Virion, Zinc ;; 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.

3lkh__assembly_2__model_1

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

Download this curve (.dat)

3lkh__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lkh__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.10 Å
Rg (electron density)	23.95 Å
Total Rg	24.88 Å
Atom count	4377
Residues	558
Excluded volume	78059 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lkh__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3lkh__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 (3)

Entity 1 Entity 1 polymer

Description description	RNA-directed RNA polymerase
Molecular weight formula_weight	64191.6 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	9891

SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLGKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAAICGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHSLSRARPRENLYFQ

Source Source

Source organism organism	Hepatitis C virus
Common name common_name	HCV
NCBI taxonomy ID ncbi_taxonomy_id	11103
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-(2-{[(1S)-1-benzyl-2-hydroxyethyl]amino}-2-oxoethoxy)-N-butyl-6-fluoro-N-methylbenzamide
Molecular weight formula_weight	416.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1120

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3lkha_
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	d3lkhb_
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	88.700 Å
Unit-cell length b length_b	107.068 Å
Unit-cell length c length_c	134.243 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	2.050 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1870
R_work r_work	0.1841
R_free r_free	0.2413

Inhibitors of Hepatitis C Virus Polymerase: Synthesis and Characterization of Novel 6-Fluoro-N-[2-Hydroxy-1(S)-Benzamides

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

3lkh__assembly_2__model_1

3lkh__assembly_2__model_1 | I(q)

3lkh__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Inhibitors of Hepatitis C Virus Polymerase: Synthesis and Characterization of Novel 6-Fluoro-N-[2-Hydroxy-1(S)-Benzamides

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

3lkh__assembly_2__model_1

3lkh__assembly_2__model_1 | I(q)

3lkh__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)