SAXSdb — 1lvm

▼

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

CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)

Tobacco etch virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 5	water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_TEV
Isoform	—
PDB entities	1, 2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 9–229； UniProt 2038–2258 Author chain B； PDBConstruct 9–229； UniProt 2038–2258 Author chain C； PDBConstruct 2–10； UniProt 2786–2794 Author chain D； PDBConstruct 2–10； UniProt 2786–2794 Author chain E； PDBConstruct 1–7； UniProt 2267–2273

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	1lvm
Deposition date deposition_date	2002-05-28
Structure title title	CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH PRODUCT
Keywords keywords	Beta Barrel, Chymotrypsin-type Cystein Protease, Enzyme-peptide Complex, 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.

1lvm__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1lvm__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1lvm__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.93 Å
Rg (electron density)	25.10 Å
Total Rg	25.84 Å
Atom count	3750
Residues	467
Excluded volume	66276 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1lvm__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1lvm__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1lvm__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
Molecular weight formula_weight	26147.6 kDa
Mutation mutation	S219D
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	4324

GHHHHHHHGESLFKGPRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQKLKFREPQREERICLVTTNFQTKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQCGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMDKP

Source Source

Source organism organism	Tobacco etch virus
NCBI taxonomy ID ncbi_taxonomy_id	12227
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
Molecular weight formula_weight	1084.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

XENLYFQSGT

Source Source

Source organism organism	Tobacco etch virus
NCBI taxonomy ID ncbi_taxonomy_id	12227
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
Molecular weight formula_weight	805.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

EATQLMN

Source Source

Source organism organism	Tobacco etch virus
NCBI taxonomy ID ncbi_taxonomy_id	12227
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	574

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1lvm.1
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.47.1.3 — Viral proteases

Domain ID domain_id	d1lvmb_
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.47.1.3 — Viral proteases

CATH v4.4 (4 domains)

Domain ID domain_id	1lvmA01
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	1lvmA02
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	1lvmB01
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	1lvmB02
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

▶

Unit-cell length a length_a	75.505 Å
Unit-cell length b length_b	75.505 Å
Unit-cell length c length_c	183.167 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.1710
R_free r_free	0.2300

CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH PRODUCT

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

CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)

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

1lvm__assembly_3__model_1

1lvm__assembly_3__model_1 | I(q)

1lvm__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH PRODUCT

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

CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)

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

1lvm__assembly_3__model_1

1lvm__assembly_3__model_1 | I(q)

1lvm__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)