SAXSdb — 6bee

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

Scaffold protein D13

Vaccinia virus WR

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	FORMIC ACID × 5 1,2-ETHANEDIOL × 4 ;(2S,16Z,18E,20S,21S,22R,23R,24R,25S,26R,27S,28E)-5,6,21,23-tetrahydroxy-27-methoxy-2,4,11,16,20,22,24,26-octamethyl-1,1 5-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)furo[2'',3'':7',8']naphtho[1',2':4,5]imidazo[1,2-a]pyridin-2 5-yl acetate ; × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D13_VACCW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–553； UniProt 1–551 Author chain B； PDBConstruct 3–553； UniProt 1–551 Author chain C； PDBConstruct 3–553； UniProt 1–551

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	6bee
Deposition date deposition_date	2017-10-25
Structure title title	Crystal structure of VACV D13 in complex with Rifaximin
Keywords keywords	poxvirus, assembly, scaffolding protein, Rifampicin resistance protein, immature virion, 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.

6bee__assembly_1__model_1

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

Download this curve (.dat)

6bee__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6bee__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.88 Å
Rg (electron density)	34.54 Å
Total Rg	35.32 Å
Atom count	12756
Residues	1613
Excluded volume	228010 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6bee__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Scaffold protein D13
Molecular weight formula_weight	62076.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	13097

GAMNNTIINSLIGGDDSIKRSNVFAVDSQIPTLYMPQYISLSGVMTNDGPDNQAIASFEIRDQYITALNHLVLSLELPEVKGMGRFGYVPYVGYKCINHVSISSCNGVIWEIEGEELYNNCINNTIALKHSGYSSELNDISIGLTPNDTIKEPSTVYVYIKTPFDVEDTFSSLKLSDSKITVTVTFNPVSDIVIRDSSFDFETFNKEFVYVPELSFIGYMVKNVQIKPSFIEKPRRVIGQINQPTATVTEVHAATSLSVYTKPYYGNTDNKFISYPGYSQDEKDYIDAYVSRLLDDLVIVSDGPPTGYPESAEIVEVPEDGIVSIQDADVYVKIDNVPDNMSVYLHTNLLMFGTRKNSFIYNISKKFSAITGTYSDATKRTIFAHISHSINIIDTSIPVSLWTSQRNVYNGDNRSAESKAKDLFINDPFIKGIDFKNKTDIISRLEVRFGNDVLYSENGPISRIYNELLTKSNNGTRTLTFNFTPKIFFRPTTITANVSRGKDKLSVRVVYSTMDVNHPIYYVQKQLVVVCNDLYKVSYDQGVSITKIMGDNN

Source Source

Source organism organism	Vaccinia virus WR
Common name common_name	VACV
NCBI taxonomy ID ncbi_taxonomy_id	10254
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	;(2S,16Z,18E,20S,21S,22R,23R,24R,25S,26R,27S,28E)-5,6,21,23-tetrahydroxy-27-methoxy-2,4,11,16,20,22,24,26-octamethyl-1,1 5-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)furo[2'',3'':7',8']naphtho[1',2':4,5]imidazo[1,2-a]pyridin-2 5-yl acetate ;
Molecular weight formula_weight	785.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	278

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Unit-cell length a length_a	191.140 Å
Unit-cell length b length_b	191.140 Å
Unit-cell length c length_c	253.270 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	36

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.110 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1980
R_work r_work	0.1970
R_free r_free	0.2180

Crystal structure of VACV D13 in complex with Rifaximin

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

Scaffold protein D13

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

6bee__assembly_1__model_1

6bee__assembly_1__model_1 | I(q)

6bee__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of VACV D13 in complex with Rifaximin

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

Scaffold protein D13

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

6bee__assembly_1__model_1

6bee__assembly_1__model_1 | I(q)

6bee__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)