SAXSdb — 3nf3

▼

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

BoNT/A

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	JTH-NB72-39 inhibitor × 1 ZINC ION × 1 NICKEL (II) ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7B8V4_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–420； UniProt 1–420

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	3nf3
Deposition date deposition_date	2010-06-09
Structure title title	Crystal structure of BoNT/A LC with JTH-NB-7239 peptide
Keywords keywords	;Botulinum neurotoxin, SNARE, BOTULISM, INHIBITION, METALLOPROTEASE, NEUROTRANSMISSION, NEUROMUSCULAR JUNCTION, HYDROLASE, MEMBRANE, METAL-BINDING, PROTEASE, SECRETED, TOXIN, HYDROLASE-HYDROLASE INHIBITOR complex ;; HYDROLASE/HYDROLASE INHIBITOR
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.

3nf3__assembly_1__model_1

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

Download this curve (.dat)

3nf3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nf3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.28 Å
Rg (electron density)	21.16 Å
Total Rg	22.18 Å
Atom count	3257
Residues	399
Excluded volume	58377 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nf3__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	BoNT/A
Molecular weight formula_weight	48704.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3343

MPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTPLVPR

Source Source

Source organism organism	Clostridium botulinum
NCBI taxonomy ID ncbi_taxonomy_id	1491
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	JTH-NB72-39 inhibitor
Molecular weight formula_weight	951.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

RRFAAMLA

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	1

Entity 4 Entity 4 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 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	86

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3nf3a_
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 (1 domains)

Domain ID domain_id	3nf3A00
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

▶

Unit-cell length a length_a	56.100 Å
Unit-cell length b length_b	189.600 Å
Unit-cell length c length_c	41.510 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	38.020 Å
R factor r_factor	0.1850
R_work r_work	0.1830
R_free r_free	0.2310

Crystal structure of BoNT/A LC with JTH-NB-7239 peptide

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

BoNT/A

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

3nf3__assembly_1__model_1

3nf3__assembly_1__model_1 | I(q)

3nf3__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of BoNT/A LC with JTH-NB-7239 peptide

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

BoNT/A

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

3nf3__assembly_1__model_1

3nf3__assembly_1__model_1 | I(q)

3nf3__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)