6l4z

Crystal structure of Zika NS2B-NS3 protease with compound 6

Method: X-RAY DIFFRACTION

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

Genome polyprotein

Zika virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （H8XX12） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （H8XX12） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （H8XX12） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （H8XX12） 4-(hydroxymethyl)benzoic acid × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_ZIKV
Isoform	—
PDB entities	1, 3, 6
Chains and sequence ranges	Author chain A； PDBConstruct 1–38； UniProt 1418–1455 Author chain E； PDBConstruct 1–38； UniProt 1418–1455 Author chain C； PDBConstruct 1–37； UniProt 1419–1455 Author chain G； PDBConstruct 1–40； UniProt 1418–1457

Genome polyprotein

Zika virus

UniProt H8XX12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （Q32ZE1） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （Q32ZE1） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （Q32ZE1） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （Q32ZE1） 4-(hydroxymethyl)benzoic acid × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H8XX12_ZIKV
Isoform	—
PDB entities	2, 4, 5, 7
Chains and sequence ranges	Author chain B； PDBConstruct 1–155； UniProt 1512–1666 Author chain D； PDBConstruct 1–153； UniProt 1514–1666 Author chain F； PDBConstruct 1–152； UniProt 1515–1666 Author chain H； PDBConstruct 1–159； UniProt 1508–1666

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	6l4z
Deposition date deposition_date	2019-10-21
Structure title title	Crystal structure of Zika NS2B-NS3 protease with compound 6
Keywords keywords	Viral protease, Protease inhibitor complex, 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.

6l4z__assembly_3__model_1

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

Download this curve (.dat)

6l4z__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6l4z__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	16.73 Å
Rg (electron density)	15.58 Å
Total Rg	16.78 Å
Atom count	1395
Residues	190
Excluded volume	24850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6l4z__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6l4z__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6l4z__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6l4z__assembly_4__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 (9)

Entity 1 Entity 1 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	4218.5 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13,2.1.1.56,2.1.1.57,2.7.7.48
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	5807

DMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLV

Source Source

Source organism organism	Zika virus
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	Genome polyprotein
Molecular weight formula_weight	16556.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKR

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	4103.5 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13,2.1.1.56,2.1.1.57,2.7.7.48
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLV

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	16370.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

TTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKR

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	16269.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

TDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKR

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	4476.8 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13,2.1.1.56,2.1.1.57,2.7.7.48
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

DMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEE

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	17043.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKR

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 non-polymer

Description description	4-(hydroxymethyl)benzoic acid
Molecular weight formula_weight	152.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	174

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6l4za_
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	d6l4zb_
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	d6l4zc_
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	d6l4zd_
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	d6l4ze_
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	d6l4zf_
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	d6l4zg_
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	d6l4zh_
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	6l4zB01
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	6l4zB02
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	6l4zD01
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	6l4zD02
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	6l4zF01
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	6l4zF02
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	6l4zH01
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	6l4zH02
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	59.549 Å
Unit-cell length b length_b	59.525 Å
Unit-cell length c length_c	214.556 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	45.760 Å
R factor r_factor	0.1912
R_work r_work	0.1798
R_free r_free	0.2261

Crystal structure of Zika NS2B-NS3 protease with compound 6

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

Genome polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Genome polyprotein

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

6l4z__assembly_3__model_1

6l4z__assembly_3__model_1 | I(q)

6l4z__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 (9)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)