SAXSdb — 2a4r

▼

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

NS3 protease/helicase

Hepatitis C virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ns4a peptide × 2 （O39914） ZINC ION × 2 ;[(N-{3-[(N-{CYCLOHEXYL[(ISOBUTOXYCARBONYL)AMINO]ACETYL}-3-CYCLOPROPYLALANYL)AMINO]-4-CYCLOPROPYL-2-OXOBUTANOYL}GLYCYL)AMINO](PHENYL)ACETIC ACID ; × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q91RS4_9HEPC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–192； UniProt 1–181 Author chain C； PDBConstruct 12–192； UniProt 1–181

Ns4a peptide

OrganismNot specified

UniProt O39914

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	NS3 protease/helicase × 2 （Q91RS4） ZINC ION × 2 ;[(N-{3-[(N-{CYCLOHEXYL[(ISOBUTOXYCARBONYL)AMINO]ACETYL}-3-CYCLOPROPYLALANYL)AMINO]-4-CYCLOPROPYL-2-OXOBUTANOYL}GLYCYL)AMINO](PHENYL)ACETIC ACID ; × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O39914_9HEPC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–21； UniProt 6–24 Author chain D； PDBConstruct 3–21； UniProt 6–24

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2a4r
Deposition date deposition_date	2005-06-29
Structure title title	HCV NS3 Protease Domain with a Ketoamide Inhibitor Covalently bound.
Keywords keywords	viral protein; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2a4r__assembly_1__model_1

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

Download this curve (.dat)

2a4r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2a4r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.00 Å
Rg (electron density)	22.28 Å
Total Rg	23.07 Å
Atom count	2776
Residues	370
Excluded volume	49782 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2a4r__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	NS3 protease/helicase
Molecular weight formula_weight	21233.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2937

MASMTGGQQMGAPITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMRSGSHHHHHH

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 polymer

Description description	Ns4a peptide
Molecular weight formula_weight	2394.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

KKGSVVIVGRIVLSGKPAIIPKK

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	;[(N-{3-[(N-{CYCLOHEXYL[(ISOBUTOXYCARBONYL)AMINO]ACETYL}-3-CYCLOPROPYLALANYL)AMINO]-4-CYCLOPROPYL-2-OXOBUTANOYL}GLYCYL)AMINO](PHENYL)ACETIC ACID ;
Molecular weight formula_weight	697.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	161

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2a4rA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2a4rA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2a4rC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2a4rC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

▶

7. Citations (6)

Hepatitis C Virus NS3-4A serine protease inhibitors: Use of a P2-P1 cyclopropyl alanine combination for improved potency.

Bioorg.Med.Chem.Lett. (2005)

PMID: 16112862 · DOI: 10.1016/j.bmcl.2005.07.009 PRIMARY

;Hepatitis C virus NS3-4A serine protease inhibitors. SAR of P2' moiety with improved potency. ;

Bioorg.Med.Chem.Lett. (2005)

PMID: 16087332 · DOI: 10.1016/j.bmcl.2005.06.091

Inhibition of the Hepatitis C Virus NS3/4A Protease. The Crystal Structures of Two protease-inhibitor complexes.

J.Biol.Chem. (2000)

PMID: 10702283 · DOI: 10.1074/jbc.275.10.7152

Complex of NS3 protease and NS4a peptide of BK strain hepatitis C virus: A 2.2A resolution structure in a hexagonal crystal form.

Protein Sci. (1998)

PMID: 9568891

Crystal Structure of the Hepatitis C Virus NS3 Protease Domain Complexed with a Synthetic NS4a Cofactor Peptide

Cell(Cambridge,Mass.) (1996)

PMID: 8861917 · DOI: 10.1016/S0092-8674(00)81351-3

The Crystal Structure of Hepatitis C Virus NS3 proteinase Reveals a Trypsin-like fold and a Structural Zinc Binding Site.

Cell(Cambridge,Mass.) (1996)

PMID: 8861916 · DOI: 10.1016/S0092-8674(00)81350-1

Unit-cell length a length_a	223.603 Å
Unit-cell length b length_b	223.603 Å
Unit-cell length c length_c	75.354 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	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2010
R_free r_free	0.2710

HCV NS3 Protease Domain with a Ketoamide Inhibitor Covalently bound.

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

NS3 protease/helicase

State in the Current Structure

Other States of the Same Protein in the Database

Ns4a peptide

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

2a4r__assembly_1__model_1

2a4r__assembly_1__model_1 | I(q)

2a4r__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (6)

HCV NS3 Protease Domain with a Ketoamide Inhibitor Covalently bound.

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

NS3 protease/helicase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ns4a peptide

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

2a4r__assembly_1__model_1

2a4r__assembly_1__model_1 | I(q)

2a4r__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (6)