SAXSdb — 2oc8

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

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	Hepatitis C virus × 2 （Q9QP06） ZINC ION × 2 BETA-MERCAPTOETHANOL × 1 boceprevir (bound form) × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9ELS8_9HEPC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–192； UniProt 1027–1207 Author chain C； PDBConstruct 12–192； UniProt 1027–1207

Hepatitis C virus

OrganismNot specified

UniProt Q9QP06

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Hepatitis C virus × 2 （Q9ELS8） ZINC ION × 2 BETA-MERCAPTOETHANOL × 1 boceprevir (bound form) × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9QP06_9HEPC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–21； UniProt 1678–1696 Author chain D； PDBConstruct 3–21； UniProt 1678–1696

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	2oc8
Deposition date deposition_date	2006-12-20
Structure title title	Structure of Hepatitis C Viral NS3 protease domain complexed with NS4A peptide and ketoamide SCH503034
Keywords keywords	Hepatitis C Virus, HCV, NS3 protease domain, ketoamide inhibitor, Viral Protein; VIRAL PROTEIN
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.

2oc8__assembly_1__model_1

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

Download this curve (.dat)

2oc8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2oc8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.94 Å
Rg (electron density)	22.24 Å
Total Rg	23.02 Å
Atom count	2797
Residues	374
Excluded volume	50216 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2oc8__assembly_1__model_1`	tetrameric （4）	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	Hepatitis C virus
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	2935

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	Hepatitis C virus
Molecular weight formula_weight	2394.0 kDa
Mutation mutation	C22S
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	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	boceprevir (bound form)
Molecular weight formula_weight	521.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2oc8A01
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	2oc8A02
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	2oc8C01
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	2oc8C02
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

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7. Citations (6)

;Discovery of the HCV NS3/4A protease inhibitor (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3- [2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]- 6,6-dimethyl-3-azabicyclo[3.1.0]hexan-2(S)-carboxamide (Sch 503034) II. Key steps in structure-based optimization. ;

J.Med.Chem. (2007)

PMID: 17444623 · DOI: 10.1021/jm060173k PRIMARY

;Depeptidization efforts on P3-P2' alpha-ketoamide inhibitors of HCV NS3-4A serine protease: effect on HCV replicon activity. ;

Bioorg.Med.Chem.Lett. (2006)

PMID: 16387495 · DOI: 10.1016/j.bmcl.2005.12.013

;Hepatitis C virus NS3-4A serine protease inhibitors: SAR of P'2 moiety with improved potency. ;

Bioorg.Med.Chem.Lett. (2005)

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

Synthesis and biological activity of macrocyclic inhibitors of hepatitis C virus (HCV) NS3 protease.

Bioorg.Med.Chem.Lett. (2005)

PMID: 16112859 · DOI: 10.1016/j.bmcl.2005.07.033

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

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

Unit-cell length a length_a	223.871 Å
Unit-cell length b length_b	223.871 Å
Unit-cell length c length_c	74.962 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	2.660 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.1920
R_free r_free	0.2780

Structure of Hepatitis C Viral NS3 protease domain complexed with NS4A peptide and ketoamide SCH503034

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

Hepatitis C virus

State in the Current Structure

Other States of the Same Protein in the Database

Hepatitis C virus

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

2oc8__assembly_1__model_1

2oc8__assembly_1__model_1 | I(q)

2oc8__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 polymer

Polymer 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) 4 domains

CATH v4.4 (4 domains)

7. Citations (6)

Structure of Hepatitis C Viral NS3 protease domain complexed with NS4A peptide and ketoamide SCH503034

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

Hepatitis C virus

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hepatitis C virus

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

2oc8__assembly_1__model_1

2oc8__assembly_1__model_1 | I(q)

2oc8__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 polymer

Polymer 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) 4 domains

CATH v4.4 (4 domains)

7. Citations (6)