SAXSdb — 1wyk

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

SINDBIS VIRUS CAPSID PROTEIN

Sindbis virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FORMYL GROUP × 1 1,4-DIETHYLENE DIOXIDE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FORMYL GROUP × 1 1,4-DIETHYLENE DIOXIDE × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	FORMYL GROUP × 1 1,4-DIETHYLENE DIOXIDE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	FORMYL GROUP × 1 1,4-DIETHYLENE DIOXIDE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLS_SINDO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–152； UniProt 114–264 Author chain B； PDBConstruct 2–152； UniProt 114–264 Author chain C； PDBConstruct 2–152； UniProt 114–264 Author chain D； PDBConstruct 2–152； UniProt 114–264

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	1wyk
Deposition date deposition_date	1998-01-12
Structure title title	SINDBIS VIRUS CAPSID PROTEIN (114-264)
Keywords keywords	COAT PROTEIN, SINDBIS, VIRUS, PROTEINASE, ALPHAVIRUS, CAPSID, DIOXANE, Viral protein, hydrolase; Viral protein, 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.

1wyk__assembly_1__model_1

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

Download this curve (.dat)

1wyk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wyk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.09 Å
Rg (electron density)	14.80 Å
Total Rg	15.93 Å
Atom count	1450
Residues	152
Excluded volume	20839 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wyk__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1wyk__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1wyk__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1wyk__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 (4)

Entity 1 Entity 1 polymer

Description description	SINDBIS VIRUS CAPSID PROTEIN
Molecular weight formula_weight	16676.8 kDa
EC 编号 ec_number	3.4.21.-
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	7213

MRLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW

Source Source

Source organism organism	Sindbis virus
NCBI taxonomy ID ncbi_taxonomy_id	11034
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FORMYL GROUP
Molecular weight formula_weight	30.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	1,4-DIETHYLENE DIOXIDE
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	469

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1wyka_
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	d1wykb_
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	d1wykc_
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	d1wykd_
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	1wykA01
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	1wykA02
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	1wykB01
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	1wykB02
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	1wykC01
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	1wykC02
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	1wykD01
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	1wykD02
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	35.980 Å
Unit-cell length b length_b	59.540 Å
Unit-cell length c length_c	71.050 Å
Unit-cell angle α angle_alpha	109.40 °
Unit-cell angle β angle_beta	101.50 °
Unit-cell angle γ angle_gamma	90.14 °
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	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2680

SINDBIS VIRUS CAPSID PROTEIN (114-264)

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

SINDBIS VIRUS CAPSID PROTEIN

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

1wyk__assembly_1__model_1

1wyk__assembly_1__model_1 | I(q)

1wyk__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (3)

SINDBIS VIRUS CAPSID PROTEIN (114-264)

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

SINDBIS VIRUS CAPSID PROTEIN

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

1wyk__assembly_1__model_1

1wyk__assembly_1__model_1 | I(q)

1wyk__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (3)