1qa7

CRYSTAL COMPLEX OF THE 3C PROTEINASE FROM HEPATITIS A VIRUS WITH ITS INHIBITOR AND IMPLICATIONS FOR THE POLYPROTEIN PROCESSING IN HAV

Method: X-RAY DIFFRACTION

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

HAV 3C PROTEINASE

Hepatitis A virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	N-(iodoacetyl)-L-valyl-L-phenylalaninamide × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	N-(iodoacetyl)-L-valyl-L-phenylalaninamide × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	N-(iodoacetyl)-L-valyl-L-phenylalaninamide × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	N-(iodoacetyl)-L-valyl-L-phenylalaninamide × 1 DIMETHYL SULFOXIDE × 1 GLYCEROL × 1 water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	N-(iodoacetyl)-L-valyl-L-phenylalaninamide × 4 DIMETHYL SULFOXIDE × 1 GLYCEROL × 1 water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	N-(iodoacetyl)-L-valyl-L-phenylalaninamide × 2 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	N-(iodoacetyl)-L-valyl-L-phenylalaninamide × 2 DIMETHYL SULFOXIDE × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_HPAV8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–217； UniProt 1519–1735 Author chain B； PDBConstruct 1–217； UniProt 1519–1735 Author chain C； PDBConstruct 1–217； UniProt 1519–1735 Author chain D； PDBConstruct 1–217； UniProt 1519–1735

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	1qa7
Deposition date deposition_date	1999-04-15
Structure title title	CRYSTAL COMPLEX OF THE 3C PROTEINASE FROM HEPATITIS A VIRUS WITH ITS INHIBITOR AND IMPLICATIONS FOR THE POLYPROTEIN PROCESSING IN HAV
Keywords keywords	;CHYMOTRYPSIN-LIKE CYSTEINE PROTEINASE VIRAL PROTEASE P'-SITE INHIBITOR, HYDROLASE, hydrolase-hydrolase inhibitor complex ;; hydrolase/hydrolase inhibitor
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.

1qa7__assembly_1__model_1

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

Download this curve (.dat)

1qa7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1qa7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.64 Å
Rg (electron density)	16.23 Å
Total Rg	17.33 Å
Atom count	1658
Residues	213
Excluded volume	29761 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1qa7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1qa7__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1qa7__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1qa7__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1qa7__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1qa7__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`1qa7__assembly_7__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 (5)

Entity 1 Entity 1 polymer

Description description	HAV 3C PROTEINASE
Molecular weight formula_weight	23828.5 kDa
Mutation mutation	C24S, F82A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7228

STLEIAGLVRKNLVQFGVGEKNGSVRWVMNALGVKDDWLLVPSHAYKFEKDYEMMEFYFNRGGTYYSISAGNVVIQSLDVGAQDVVLMKVPTIPKFRDITQHFIKKGDVPRALNRLATLVTTVNGTPMLISEGPLKMEEKATYVHKKNDGTTVDLTVDQAWRGKGEGLPGMCGGALVSSNQSIQNAILGIHVAGGNSILVAKLVTQEMFQNIDKKIE

Source Source

Source organism organism	Hepatitis A virus
NCBI taxonomy ID ncbi_taxonomy_id	12092
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N-(iodoacetyl)-L-valyl-L-phenylalaninamide
Molecular weight formula_weight	431.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	514

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1qa7a_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.4 — Viral cysteine protease of trypsin fold

Domain ID domain_id	d1qa7b_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.4 — Viral cysteine protease of trypsin fold

Domain ID domain_id	d1qa7c_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.4 — Viral cysteine protease of trypsin fold

Domain ID domain_id	d1qa7d_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.4 — Viral cysteine protease of trypsin fold

CATH v4.4 (8 domains)

Domain ID domain_id	1qa7A01
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	1qa7A02
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	1qa7B01
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	1qa7B02
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	1qa7C01
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	1qa7C02
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	1qa7D01
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	1qa7D02
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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Unit-cell length a length_a	50.562 Å
Unit-cell length b length_b	78.357 Å
Unit-cell length c length_c	105.287 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2140
R_work r_work	0.2040
R_free r_free	0.2980

CRYSTAL COMPLEX OF THE 3C PROTEINASE FROM HEPATITIS A VIRUS WITH ITS INHIBITOR AND IMPLICATIONS FOR THE POLYPROTEIN PROCESSING IN HAV

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

HAV 3C PROTEINASE

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

1qa7__assembly_1__model_1

1qa7__assembly_1__model_1 | I(q)

1qa7__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (5)

CRYSTAL COMPLEX OF THE 3C PROTEINASE FROM HEPATITIS A VIRUS WITH ITS INHIBITOR AND IMPLICATIONS FOR THE POLYPROTEIN PROCESSING IN HAV

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

HAV 3C PROTEINASE

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

1qa7__assembly_1__model_1

1qa7__assembly_1__model_1 | I(q)

1qa7__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (5)