5gj4

Structure of NS2B-NS3 Protease from Zika Virus caught after self-cleavage

Method: X-RAY DIFFRACTION

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

Serine protease subunit NS2B

Zika virus (strain Mr 766)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CHLORIDE ION × 1 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	CHLORIDE ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A142IX72_ZIKV
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 5–56； UniProt 1411–1462 Author chain A； PDBConstruct 57–61； UniProt 1492–1496 Author chain C； PDBConstruct 5–56； UniProt 1411–1462 Author chain C； PDBConstruct 57–61； UniProt 1492–1496 Author chain E； PDBConstruct 5–56； UniProt 1411–1462 Author chain E； PDBConstruct 57–61； UniProt 1492–1496 Author chain G； PDBConstruct 5–56； UniProt 1411–1462 Author chain G； PDBConstruct 57–61； UniProt 1492–1496 Author chain B； PDBConstruct 1–177； UniProt 1497–1673 Author chain D； PDBConstruct 1–177； UniProt 1497–1673 Author chain F； PDBConstruct 1–177； UniProt 1497–1673 Author chain H； PDBConstruct 1–177； UniProt 1497–1673

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	5gj4
Deposition date deposition_date	2016-06-27
Structure title title	Structure of NS2B-NS3 Protease from Zika Virus caught after self-cleavage
Keywords keywords	Zika virus protease, antiviral drug discovery, HYDROLASE; HYDROLASE
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.

5gj4__assembly_1__model_1

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

Download this curve (.dat)

5gj4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5gj4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.28 Å
Rg (electron density)	22.68 Å
Total Rg	23.44 Å
Atom count	2948
Residues	391
Excluded volume	52237 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5gj4__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5gj4__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Serine protease subunit NS2B
Molecular weight formula_weight	6721.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	7043

GSHMTGKSVDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEEDGPPMREKTGKR

Source Source

Source organism organism	Zika virus (strain Mr 766)
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Serine protease NS3
Molecular weight formula_weight	18980.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

SGALWDVPAPKEVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKREEETPVE

Source Source

Source organism organism	Zika virus (strain Mr 766)
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1138

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5gj4a1
Class class	g — Small proteins
Fold Fold fold	g.96 — Flavivirus non-structural protein NS2B-like
Superfamily Superfamily superfamily	g.96.1 — Flavivirus non-structural protein NS2B-like
Family Family family	g.96.1.0 — automated matches

Domain ID domain_id	d5gj4b_
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	d5gj4c1
Class class	g — Small proteins
Fold Fold fold	g.96 — Flavivirus non-structural protein NS2B-like
Superfamily Superfamily superfamily	g.96.1 — Flavivirus non-structural protein NS2B-like
Family Family family	g.96.1.0 — automated matches

Domain ID domain_id	d5gj4d_
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	d5gj4e1
Class class	g — Small proteins
Fold Fold fold	g.96 — Flavivirus non-structural protein NS2B-like
Superfamily Superfamily superfamily	g.96.1 — Flavivirus non-structural protein NS2B-like
Family Family family	g.96.1.0 — automated matches

Domain ID domain_id	d5gj4f_
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	d5gj4g1
Class class	g — Small proteins
Fold Fold fold	g.96 — Flavivirus non-structural protein NS2B-like
Superfamily Superfamily superfamily	g.96.1 — Flavivirus non-structural protein NS2B-like
Family Family family	g.96.1.0 — automated matches

Domain ID domain_id	d5gj4h_
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 (8 domains)

Domain ID domain_id	5gj4B01
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	5gj4B02
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	5gj4D01
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	5gj4D02
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	5gj4F01
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	5gj4F02
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	5gj4H01
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	5gj4H02
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	88.790 Å
Unit-cell length b length_b	88.790 Å
Unit-cell length c length_c	138.100 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	12

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	1.839 Å
Low-resolution limit resolution_low	31.496 Å
R factor r_factor	0.1812
R_work r_work	0.1694
R_free r_free	0.1953

Structure of NS2B-NS3 Protease from Zika Virus caught after self-cleavage

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

Serine protease subunit NS2B

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

5gj4__assembly_1__model_1

5gj4__assembly_1__model_1 | I(q)

5gj4__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of NS2B-NS3 Protease from Zika Virus caught after self-cleavage

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

Serine protease subunit NS2B

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

5gj4__assembly_1__model_1

5gj4__assembly_1__model_1 | I(q)

5gj4__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)