SAXSdb — 3d3x

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

Type E botulinum toxin

Clostridium butyricum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SNAP-25 substrate peptide × 1 ZINC ION × 1 SULFATE ION × 6 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SNAP-25 substrate peptide × 1 ZINC ION × 1 SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9K395_CLOBU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–421； UniProt 2–422 Author chain B； PDBConstruct 1–421； UniProt 2–422

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	3d3x
Deposition date deposition_date	2008-05-13
Structure title title	Crystal structure of botulinum neurotoxin serotype E catalytic domain in complex with SNAP-25 substrate peptide
Keywords keywords	BoNT E, SNAP-25, Enzyme-substrate complex, HYDROLASE, HYDROLASE-HYDROLASE SUBSTRATE COMPLEX; HYDROLASE/HYDROLASE SUBSTRATE
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.

3d3x__assembly_1__model_1

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

Download this curve (.dat)

3d3x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d3x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.18 Å
Rg (electron density)	22.14 Å
Total Rg	23.08 Å
Atom count	3315
Residues	410
Excluded volume	58904 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d3x__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3d3x__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Type E botulinum toxin
Molecular weight formula_weight	48673.8 kDa
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	6883

PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPTSLKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSIAIVTFSPEYSFRFNDNSMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTITQKQNPLITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTYIGQYKYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFCKNIVSVKGIRHHHHHH

Source Source

Source organism organism	Clostridium butyricum
NCBI taxonomy ID ncbi_taxonomy_id	1492
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SNAP-25 substrate peptide
Molecular weight formula_weight	546.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

RIMEX

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	251

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3d3xa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.7 — Clostridium neurotoxins, catalytic domain

Domain ID domain_id	d3d3xb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.7 — Clostridium neurotoxins, catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id	3d3xA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1240 — Zincin-like
Homologous superfamily homologous superfamily	10 — Metalloproteases ("zincins"), catalytic domain like

Domain ID domain_id	3d3xB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1240 — Zincin-like
Homologous superfamily homologous superfamily	10 — Metalloproteases ("zincins"), catalytic domain like

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Unit-cell length a length_a	89.410 Å
Unit-cell length b length_b	144.738 Å
Unit-cell length c length_c	83.303 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	33.480 Å
R factor r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.2880

Crystal structure of botulinum neurotoxin serotype E catalytic domain in complex with SNAP-25 substrate peptide

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

Type E botulinum toxin

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

3d3x__assembly_1__model_1

3d3x__assembly_1__model_1 | I(q)

3d3x__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of botulinum neurotoxin serotype E catalytic domain in complex with SNAP-25 substrate peptide

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

Type E botulinum toxin

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

3d3x__assembly_1__model_1

3d3x__assembly_1__model_1 | I(q)

3d3x__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)