SAXSdb — 6w5l

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

3C-LIKE PROTEASE

Norwalk virus (strain GI/Human/United States/Norwalk/1968)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;(2~{S})-~{N}-[(1~{R})-1-[bis($l^{1}-oxidanyl)-methoxy-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[[2-(3-chlorophenyl)-2-methyl-propoxy]-oxidanylidene-methyl]amino]-4-methyl-pentanamide ; × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;(2~{S})-~{N}-[(1~{R})-1-[bis($l^{1}-oxidanyl)-methoxy-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[[2-(3-chlorophenyl)-2-methyl-propoxy]-oxidanylidene-methyl]amino]-4-methyl-pentanamide ; × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	;(2~{S})-~{N}-[(1~{R})-1-[bis($l^{1}-oxidanyl)-methoxy-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[[2-(3-chlorophenyl)-2-methyl-propoxy]-oxidanylidene-methyl]amino]-4-methyl-pentanamide ; × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	;(2~{S})-~{N}-[(1~{R})-1-[bis($l^{1}-oxidanyl)-methoxy-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[[2-(3-chlorophenyl)-2-methyl-propoxy]-oxidanylidene-methyl]amino]-4-methyl-pentanamide ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_NVN68
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–188； UniProt 1101–1281 Author chain B； PDBConstruct 8–188； UniProt 1101–1281 Author chain C； PDBConstruct 8–188； UniProt 1101–1281 Author chain D； PDBConstruct 8–188； UniProt 1101–1281

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	6w5l
Deposition date deposition_date	2020-03-13
Structure title title	2.1 A resolution structure of Norovirus 3CL protease in complex with inhibitor 7g
Keywords keywords	PROTEASE, Norovirus 3CL protease, Inhhibitors, 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.

6w5l__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6w5l__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6w5l__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	15.74 Å
Rg (electron density)	14.66 Å
Total Rg	15.85 Å
Atom count	1234
Residues	166
Excluded volume	22149 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6w5l__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6w5l__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6w5l__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6w5l__assembly_4__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	3C-LIKE PROTEASE
Molecular weight formula_weight	20133.1 kDa
EC 编号 ec_number	3.6.1.15,3.4.22.66,2.7.7.48
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	5025

HHHHHHHAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAIHQAGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRIQGRLVHGQSGMLLTGANAKGMDLGTIPGDCGAPYVHKRGNDWVVCGVHAAATKSGNTVVCAVQAGEGETALE

Source Source

Source organism organism	Norwalk virus (strain GI/Human/United States/Norwalk/1968)
Common name common_name	Hu/NV/NV/1968/US
NCBI taxonomy ID ncbi_taxonomy_id	524364
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	;(2~{S})-~{N}-[(1~{R})-1-[bis($l^{1}-oxidanyl)-methoxy-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[[2-(3-chlorophenyl)-2-methyl-propoxy]-oxidanylidene-methyl]amino]-4-methyl-pentanamide ;
Molecular weight formula_weight	604.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6w5la1
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	d6w5la2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6w5lb1
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	d6w5lb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6w5lc1
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	d6w5lc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6w5ld1
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	d6w5ld2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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Unit-cell length a length_a	37.435 Å
Unit-cell length b length_b	37.859 Å
Unit-cell length c length_c	115.535 Å
Unit-cell angle α angle_alpha	91.65 °
Unit-cell angle β angle_beta	96.44 °
Unit-cell angle γ angle_gamma	95.44 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	36.210 Å
R factor r_factor	0.2068
R_work r_work	0.2038
R_free r_free	0.2668

2.1 A resolution structure of Norovirus 3CL protease in complex with inhibitor 7g

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

3C-LIKE PROTEASE

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

6w5l__assembly_2__model_1

6w5l__assembly_2__model_1 | I(q)

6w5l__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)

2.1 A resolution structure of Norovirus 3CL protease in complex with inhibitor 7g

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

3C-LIKE PROTEASE

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

6w5l__assembly_2__model_1

6w5l__assembly_2__model_1 | I(q)

6w5l__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)