SAXSdb — 6g5k

▼

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

Botulinum neurotoxin type B

Clostridium botulinum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Synaptotagmin-1 × 1 （P21579） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Synaptotagmin-1 × 1 （P21579） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BXB_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–459； UniProt 857–1291 Author chain B； PDBConstruct 25–459； UniProt 857–1291

Synaptotagmin-1

OrganismNot specified

UniProt P21579

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Botulinum neurotoxin type B × 1 （P10844） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Botulinum neurotoxin type B × 1 （P10844） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYT1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 33； PDBConstruct 1–21； UniProt 33–53 Author chain C； PDBConstruct 1–21； UniProt 33–53

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6g5k
Deposition date deposition_date	2018-03-29
Structure title title	Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1
Keywords keywords	botulinum toxin, neurotoxin, protein engineering, receptor binding, TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6g5k__assembly_1__model_1

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

Download this curve (.dat)

6g5k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6g5k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.83 Å
Rg (electron density)	24.98 Å
Total Rg	25.91 Å
Atom count	3723
Residues	437
Excluded volume	66488 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6g5k__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6g5k__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Botulinum neurotoxin type B
Molecular weight formula_weight	55157.1 kDa
EC 编号 ec_number	3.4.24.69
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7923

MGSSHHHHHHSSGLVPRGSHMASMNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNSQSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTELQ

Source Source

Source organism organism	Clostridium botulinum
NCBI taxonomy ID ncbi_taxonomy_id	1491
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Synaptotagmin-1
Molecular weight formula_weight	2471.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,33

GEGKEDAFSKLKEKFMNELHK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	439

▶

Unit-cell length a length_a	48.300 Å
Unit-cell length b length_b	212.790 Å
Unit-cell length c length_c	52.910 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	53.250 Å
R factor r_factor	0.1957
R_work r_work	0.1936
R_free r_free	0.2354

Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1

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

Botulinum neurotoxin type B

State in the Current Structure

Other States of the Same Protein in the Database

Synaptotagmin-1

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

6g5k__assembly_1__model_1

6g5k__assembly_1__model_1 | I(q)

6g5k__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1

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

Botulinum neurotoxin type B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Synaptotagmin-1

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

6g5k__assembly_1__model_1

6g5k__assembly_1__model_1 | I(q)

6g5k__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)