SAXSdb — 5h6v

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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 homooligomer	Homooligomer	Protein 2	(S)-2-acetamido-6-amino-N-((S)-5-guanidino-1-oxopentan-2-yl)hexanamide × 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	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 2–52； UniProt 1411–1462 Author chain B； PDBConstruct 2–178； 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	5h6v
Deposition date deposition_date	2016-11-15
Structure title title	Structure of Zika virus protease in complex with a dipeptide inhibitor
Keywords keywords	SERINE PROTEASE, NON-STRUCTURAL PROTEIN 3, VIRAL PROTEIN-INHIBITOR complex; VIRAL PROTEIN/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.

5h6v__assembly_1__model_1

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

Download this curve (.dat)

5h6v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5h6v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.85 Å
Rg (electron density)	15.61 Å
Total Rg	16.74 Å
Atom count	1453
Residues	193
Excluded volume	25651 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5h6v__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	5750.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1474

MTGKSVDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEEGPPMRE

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	19009.6 kDa
Mutation mutation	R29K
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSGALWDVPAPKEVKKGETTDGVYRVMTRKLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKREEETPVE

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	(S)-2-acetamido-6-amino-N-((S)-5-guanidino-1-oxopentan-2-yl)hexanamide
Molecular weight formula_weight	328.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5h6va_
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	d5h6vb_
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 (2 domains)

Domain ID domain_id	5h6vB01
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	5h6vB02
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	42.330 Å
Unit-cell length b length_b	42.330 Å
Unit-cell length c length_c	214.758 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 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	2.422 Å
Low-resolution limit resolution_low	42.330 Å
R factor r_factor	0.1944
R_work r_work	0.1912
R_free r_free	0.2442

Structure of Zika virus protease in complex with a dipeptide inhibitor

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5h6v__assembly_1__model_1

5h6v__assembly_1__model_1 | I(q)

5h6v__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of Zika virus protease in complex with a dipeptide inhibitor

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5h6v__assembly_1__model_1

5h6v__assembly_1__model_1 | I(q)

5h6v__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)