SAXSdb — 5zmq

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

Serine protease subunit NS2B

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	Serine protease NS3 × 1 （H8XX12） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Serine protease NS3 × 1 （H8XX12） peptide PAC-DLY-DLY-DAR × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Serine protease NS3 × 1 （H8XX12） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Serine protease NS3 × 1 （H8XX12） peptide PAC-DLY-DLY-DAR × 1 water × 3	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
Chains and sequence ranges	Author chain A； PDBConstruct 3–53； UniProt 1414–1464 Author chain C； PDBConstruct 3–53； UniProt 1414–1464 Author chain E； PDBConstruct 3–53； UniProt 1414–1464 Author chain G； PDBConstruct 3–53； UniProt 1414–1464

Serine protease NS3

Zika virus (strain Mr 766)

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	Serine protease subunit NS2B × 1 （Q32ZE1） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Serine protease subunit NS2B × 1 （Q32ZE1） peptide PAC-DLY-DLY-DAR × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Serine protease subunit NS2B × 1 （Q32ZE1） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Serine protease subunit NS2B × 1 （Q32ZE1） peptide PAC-DLY-DLY-DAR × 1 water × 3	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
Chains and sequence ranges	Author chain B； PDBConstruct 2–178； UniProt 1497–1673 Author chain D； PDBConstruct 2–178； UniProt 1497–1673 Author chain F； PDBConstruct 2–178； UniProt 1497–1673 Author chain H； 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	5zmq
Deposition date deposition_date	2018-04-05
Structure title title	Crystal structure of Zika NS3 protease with phenylacetyl-Lys-Lys-Arg-COOH inhibitor
Keywords keywords	Viral protease, Serine protease, non-structural protein 3, Zika protease, VIRAL PROTEIN, 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.

5zmq__assembly_1__model_1

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

Download this curve (.dat)

5zmq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5zmq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.80 Å
Rg (electron density)	15.53 Å
Total Rg	16.65 Å
Atom count	1405
Residues	191
Excluded volume	24796 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5zmq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5zmq__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5zmq__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5zmq__assembly_4__model_1`	trimeric （3）	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	5865.4 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13
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	6187

MTGKSVDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEEDGPPMRE

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	Serine protease NS3
Molecular weight formula_weight	19021.5 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

GSGALWDVPAPKEVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKSGRVIGLYGNGVVIKNGSYVSAITQGKREEETPVE

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 polymer

Description description	peptide PAC-DLY-DLY-DAR
Molecular weight formula_weight	549.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(D)
Chain IDs strand_id	I,K

XKKR

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	499

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5zmqB01
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	5zmqB02
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	5zmqD01
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	5zmqD02
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	5zmqF01
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	5zmqF02
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	5zmqH01
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	5zmqH02
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	60.150 Å
Unit-cell length b length_b	60.330 Å
Unit-cell length c length_c	214.070 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.987 Å
Low-resolution limit resolution_low	57.907 Å
R factor r_factor	0.1750
R_work r_work	0.1705
R_free r_free	0.2012

Crystal structure of Zika NS3 protease with phenylacetyl-Lys-Lys-Arg-COOH inhibitor

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

Serine protease NS3

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

5zmq__assembly_1__model_1

5zmq__assembly_1__model_1 | I(q)

5zmq__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 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of Zika NS3 protease with phenylacetyl-Lys-Lys-Arg-COOH inhibitor

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

Serine protease NS3

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

5zmq__assembly_1__model_1

5zmq__assembly_1__model_1 | I(q)

5zmq__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 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)