SAXSdb — 1f31

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

BOTULINUM NEUROTOXIN TYPE B

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-alpha-D-glucopyranose × 1 ZINC ION × 1 SULFATE ION × 1 water × 1	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 1–1290； UniProt 1–1290

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	1f31
Deposition date deposition_date	2000-05-31
Structure title title	CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH A TRISACCHARIDE
Keywords keywords	botulinum, zinc, metalloprotease, transmembrane, neurotoxin, complex, ganglioside, TOXIN; TOXIN
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.

1f31__assembly_1__model_1

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

Download this curve (.dat)

1f31__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1f31__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.67 Å
Rg (electron density)	40.53 Å
Total Rg	40.67 Å
Atom count	10486
Residues	1280
Excluded volume	187530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1f31__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	BOTULINUM NEUROTOXIN TYPE B
Molecular weight formula_weight	150833.4 kDa
EC 编号 ec_number	3.4.24.69
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10584

PVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYTFGYKPEDFNKSSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIINGIPYLGDRRVPLEEFNTNIASVTVNKLISNPGEVERKKGIFANLIIFGPGPVLNENETIDIGIQNHFASREGFGGIMQMKFCPEYVSVFNNVQENKGASIFNRRGYFSDPALILMHELIHVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQNFRGIVDRLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKSLMFGFTETNIAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKDMEKEYRGQNKAINKQAYEEISKEHLAVYKIQMCKSVKAPGICIDVDNEDLFFIADKNSFSDDLSKNERIEYNTQSNYIENDFPINELILDTDLISKIELPSENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYLYSQTFPLDIRDISLTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIVNDFVIEANKSNTMDKIADISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEFIPELLIPVVGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQWLSTVNTQFYTIKEGMYKALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDNINNFINGCSVSYLMKKMIPLAVEKLLDFDNTLKKNLLNYIDENKLYLIGSAEYEKSKVNKYLKTIMPFDLSIYTNDTILIEMFNKYNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNSQSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTE

Entity 2 Entity 2 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	633.6 kDa
Source method src_method	man
Copy count entity_count	1

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	SULFATE ION
Molecular weight formula_weight	96.1 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	98

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1f31a1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.6 — Clostridium neurotoxins, the second last domain

Domain ID domain_id	d1f31a2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.4 — STI-like
Family Family family	b.42.4.2 — Clostridium neurotoxins, C-terminal domain

Domain ID domain_id	d1f31a3
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	d1f31a4
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.2 — Clostridium neurotoxins, 'coiled-coil' domain
Family Family family	h.4.2.1 — Clostridium neurotoxins, 'coiled-coil' domain

CATH v4.4 (4 domains)

Domain ID domain_id	1f31A01
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	1f31A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1120 — Clostridium botulinum neurotoxin B, "coiled-coil" domain
Homologous superfamily homologous superfamily	10 — Clostridium botulinum neurotoxin b, "coiled-coil" domain

Domain ID domain_id	1f31A03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1f31A04
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	76.300 Å
Unit-cell length b length_b	123.650 Å
Unit-cell length c length_c	95.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2130
R_work r_work	0.2120
R_free r_free	0.2700

CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH A TRISACCHARIDE

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1f31__assembly_1__model_1

1f31__assembly_1__model_1 | I(q)

1f31__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

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)

CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH A TRISACCHARIDE

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1f31__assembly_1__model_1

1f31__assembly_1__model_1 | I(q)

1f31__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

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)