2w2d

Crystal Structure of a Catalytically Active, Non-toxic Endopeptidase Derivative of Clostridium botulinum Toxin A

Method: X-RAY DIFFRACTION

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

BOTULINUM NEUROTOXIN A LIGHT CHAIN

CLOSTRIDIUM BOTULINUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 ZINC ION × 1 CHLORIDE ION × 2 GLYCEROL × 5 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 ZINC ION × 1 CHLORIDE ION × 1 ACETATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BXA1_CLOBH
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 5–446； UniProt 1–442 Author chain C； PDBConstruct 5–446； UniProt 1–442 Author chain B； PDBConstruct 1–431； UniProt 447–877 Author chain D； PDBConstruct 1–431； UniProt 447–877

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	2w2d
Deposition date deposition_date	2008-10-29
Structure title title	Crystal Structure of a Catalytically Active, Non-toxic Endopeptidase Derivative of Clostridium botulinum Toxin A
Keywords keywords	;METALLOPROTEASE, MEMBRANE DOMAIN, PROTEIN ENGINEERING, NEUROTOXIN, METAL-BINDING, TRANSMEMBRANE, PHARMACEUTICAL, HYDROLASE, ZINC PROTEASE, MIXED ALPHA AND BETA, BONT, MEMBRANE, SECRETED, PROTEASE ;; HYDROLASE
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.

2w2d__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2w2d__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2w2d__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.23 Å
Rg (electron density)	30.47 Å
Total Rg	31.19 Å
Atom count	6846
Residues	844
Excluded volume	122390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2w2d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2w2d__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 (8)

Entity 1 Entity 1 polymer

Description description	BOTULINUM NEUROTOXIN A LIGHT CHAIN
Molecular weight formula_weight	51510.2 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,C
Atom count atom_count	14160

EFGSMEFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLFEFYKLLCVDGIITSKTKSLIEGR

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	BOTULINUM NEUROTOXIN A HEAVY CHAIN
Molecular weight formula_weight	49544.8 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	B,D

NKALNLQCIKVNNWDLFFSPSEDNFTNDLNKGEEITSDTNIEAAEENISLDLIQQYYLTFNFDNEPENISIENLSSDIIGQLELMPNIERFPNGKKYELDKYTMFHYLRAQEFEHGKSRIALTNSVNEALLNPSRVYTFFSSDYVKKVNKATEAAMFLGWVEQLVYDFTDETSEVSTTDKIADITIIIPYIGPALNIGNMLYKDDFVGALIFSGAVILLEFIPEIAIPVLGTFALVSYIANKVLTVQTIDNALSKRNEKWDEVYKYIVTNWLAKVNTQIDLIRKKMKEALENQAEATKAIINYQYNQYTEEEKNNINFNIDDLSSKLNESINKAMININKFLNQCSVSYLMNSMIPYGVKRLEDFDASLKDALLKYIYDNRGTLIGQVDRLKDKVNNTLSTDIPFQLSKYVDNQRLLSTFTEYIKNIINTS

Source Source

Source organism organism	CLOSTRIDIUM BOTULINUM
NCBI taxonomy ID ncbi_taxonomy_id	1491
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	308

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2w2db1
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.92.1.0 — automated matches

Domain ID domain_id	d2w2db2
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

Domain ID domain_id	d2w2db3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2w2dd1
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.92.1.0 — automated matches

Domain ID domain_id	d2w2dd2
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

Domain ID domain_id	d2w2dd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	2w2dA00
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	2w2dB00
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	2w2dC00
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	2w2dD01
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

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Unit-cell length a length_a	78.365 Å
Unit-cell length b length_b	156.909 Å
Unit-cell length c length_c	211.651 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.590 Å
Low-resolution limit resolution_low	49.110 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2530

Crystal Structure of a Catalytically Active, Non-toxic Endopeptidase Derivative of Clostridium botulinum Toxin A

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

BOTULINUM NEUROTOXIN A LIGHT CHAIN

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

2w2d__assembly_2__model_1

2w2d__assembly_2__model_1 | I(q)

2w2d__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of a Catalytically Active, Non-toxic Endopeptidase Derivative of Clostridium botulinum Toxin A

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

BOTULINUM NEUROTOXIN A LIGHT CHAIN

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

2w2d__assembly_2__model_1

2w2d__assembly_2__model_1 | I(q)

2w2d__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)