SAXSdb — 1yvf

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

HCV NS5B 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	PHOSPHATE ION × 1 CHLORIDE ION × 1 (2Z)-2-(BENZOYLAMINO)-3-[4-(2-BROMOPHENOXY)PHENYL]-2-PROPENOIC ACID × 1 GLYCEROL × 4 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 2 CHLORIDE ION × 2 (2Z)-2-(BENZOYLAMINO)-3-[4-(2-BROMOPHENOXY)PHENYL]-2-PROPENOIC ACID × 2 GLYCEROL × 8 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O93077_9HEPC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–571； 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	1yvf
Deposition date deposition_date	2005-02-15
Structure title title	Hepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor PHA-00729145
Keywords keywords	NS5B, polymerase, HCV, fingers, palm, thumb, 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.

1yvf__assembly_1__model_1

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

Download this curve (.dat)

1yvf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yvf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.03 Å
Rg (electron density)	23.98 Å
Total Rg	24.89 Å
Atom count	4448
Residues	564
Excluded volume	79396 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yvf__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yvf__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	HCV NS5B POLYMERASE
Molecular weight formula_weight	64382.1 kDa
EC 编号 ec_number	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	4676

MSMSYTWTGALITPCAAEESKLPINALSNSLLRHHNLVYSTTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDVRSLSSRAVNHIRSVWKDLLEDTDTPIQTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKAKKCPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYVGGPMTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTVPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRAKLLSQGGRAAICGKYLFNWAVRTKLKLTPIPAASRLLLSGWFVAGYSGGDIYHSLSRARPRHHHHHH

Source Source

Source organism organism	Hepatitis C virus
NCBI taxonomy ID ncbi_taxonomy_id	11103
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	(2Z)-2-(BENZOYLAMINO)-3-[4-(2-BROMOPHENOXY)PHENYL]-2-PROPENOIC ACID
Molecular weight formula_weight	438.3 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	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	228

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1yvfa_
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

CATH v4.4 (1 domains)

Domain ID domain_id	1yvfA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

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Unit-cell length a length_a	90.879 Å
Unit-cell length b length_b	90.879 Å
Unit-cell length c length_c	188.516 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2400
R_work r_work	0.2400
R_free r_free	0.3030

Hepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor PHA-00729145

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

HCV NS5B 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

1yvf__assembly_1__model_1

1yvf__assembly_1__model_1 | I(q)

1yvf__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

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (2)

Hepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor PHA-00729145

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

HCV NS5B 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

1yvf__assembly_1__model_1

1yvf__assembly_1__model_1 | I(q)

1yvf__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

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (2)