SAXSdb — 1e1h

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

BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN

CLOSTRIDIUM BOTULINUM

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 10–250 Chain B； UniProt 251–416 Chain C； UniProt 10–250 Chain D； UniProt 251–416	Fragment：RESIDUES 10-250 Fragment：RESIDUES 252-416 Mutation：YES	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；HANGING DROP VAPOUR DIFFUSION, DROP: 4UL 5MG/ML PROTEIN & 2UL WELL. PROTEIN: 0.05M TRIS PH 8.0,10% GLYCEROL, 0.1% TRITON X-100,1.0MM 2-ME,4% XYLITOL. WELL: 0.2M (NH4)2SO4,0.1M NAOAC PH 4.6, 25% PEG4000.	Resolution 1.80 Å R-free 0.237

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1E1H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2G7K Structure of the Light Chain of Botulinum Neurotoxin, Serotype A Bound to small Molecule Inhibitors Deposited 2006-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–425（424 aa） Fragment：Light Chain A, residues 2-425	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；0.1M HEPES buffer, 30% PEG1500, 0.1M NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.80 Å R-free 0.265
2G7K Structure of the Light Chain of Botulinum Neurotoxin, Serotype A Bound to small Molecule Inhibitors Deposited 2006-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–425（424 aa） Fragment：Light Chain A, residues 2-425	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；0.1M HEPES buffer, 30% PEG1500, 0.1M NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.80 Å R-free 0.265
2G7N Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to small Molecule Inhibitors Deposited 2006-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–425（424 aa） Fragment：Light Chain A, residues 2-425	Not recorded	ZN ZINC ION × 1 AG SILVER ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M Sodium cacodylate, 28% PEG4K, 0.2M ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.90 Å R-free 0.248
2G7P Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule Inhibitors Deposited 2006-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–425（424 aa） Fragment：Light Chain A, residues 2-425	Mutation：R362A, Y365F	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1M Sodium Citrate, 24% PEG4K, 0.2M Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.30 Å R-free 0.275
2G7P Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule Inhibitors Deposited 2006-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–425（424 aa） Fragment：Light Chain A, residues 2-425	Mutation：R362A, Y365F	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1M Sodium Citrate, 24% PEG4K, 0.2M Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.30 Å R-free 0.275
2G7Q Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule Inhibitors Deposited 2006-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–425（424 aa） Fragment：Light Chain A, residues 2-425	Mutation：R362A, Y365F	ZN ZINC ION × 1 AHL N-HYDROXY-L-ARGININAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1M Sodium Citrate, PEG4K, 0.2 M Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.41 Å R-free 0.261
2G7Q Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule Inhibitors Deposited 2006-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–425（424 aa） Fragment：Light Chain A, residues 2-425	Mutation：R362A, Y365F	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1M Sodium Citrate, PEG4K, 0.2 M Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.41 Å R-free 0.261
5MOY Crystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C Deposited 2016-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 871–1296（426 aa） Fragment：UNP residues 871-1296	Not recorded	EDO 1,2-ETHANEDIOL × 1 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；285 K；20% PEG 8000, 65 mM Hepes	Resolution 2.30 Å R-free 0.251
6ES1 Crystal structure of the binding domain from botulinum neurotoxin A2 bound to extracellular domain of human receptor SV2C Deposited 2017-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 874–1296（423 aa） Fragment：Binding domain, UNP residues 874-1296	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.160 mM HcA2 (8.27 mg/mL), 0.160 mM SV2CL4 (2.24 mg/mL), 2 mM Sialylated Thomsen-Friedenreich carbohydrate antigen (Sialyl-T). Reservoir solution: 200 mM CaCl2, 100 mM MES pH 6.0, 20 % PEG 6000	Resolution 2.00 Å R-free 0.230

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BXA2_CLOBO
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 47–287； UniProt 10–250 Author chain C； PDBConstruct 47–287； UniProt 10–250 Author chain B； PDBConstruct 1–166； UniProt 251–416 Author chain D； PDBConstruct 1–166； UniProt 251–416

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	1e1h
Deposition date deposition_date	2000-05-08
Structure title title	Crystal Structure of recombinant Botulinum Neurotoxin Type A Light Chain, self-inhibiting Zn endopeptidase.
Keywords keywords	NEUROTOXIN, ZN-ENDOPEPTIDASE, COMPLEX, SUBSTRATE BOUND, BOTULINUM, INHIBITOR BOUND, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.79 Å
Radius of gyration Rg (electron density) rg_electron	32.60 Å
Forward intensity I(0) i0	125817000.00
Molecular weight molecular_weight	91487.0 kDa
Excluded volume excluded_volume	115220 Å³
Envelope volume envelope_volume	142750 Å³
Hydration-shell volume shell_volume	37675 Å³
Envelope diameter envelope_diameter	114.7 Å
Shell Rg shell_rg	38.10 Å
Envelope Rg envelope_rg	32.55 Å
Shape Rg shape_rg	32.55 Å
Total Rg total_rg	33.21 Å
Total atoms total_atoms	6462
Residues n_residues	799
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	107.3 Å
Rg (real space) rg_real	32.97 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	1.2580e+08
I(0) uncertainty (real space) i0_real_error	2.1030e+06
Rg (reciprocal space) rg_reciprocal	32.90 Å
I(0) (reciprocal space) i0_reciprocal	125800000.0000
Solution quality estimate total_estimate	0.8644
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.3 Å
Skewness Skewness skewness	0.435
Kurtosis Kurtosis kurtosis	-0.442
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29260000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.717

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN
Molecular weight formula_weight	32153.0 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	7230

MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMAYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHDVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAEHRLYGIAINPNRVFKVNTNAY

来源 Source

来源生物 organism	CLOSTRIDIUM BOTULINUM
NCBI Class编号 ncbi_taxonomy_id	1491
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN
Molecular weight formula_weight	20560.1 kDa
EC 编号 ec_number	3.4.24.69
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

YEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDVASTLNKAKSIIGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVNFFKVINRKTYLNFDKAVFRINIVPDENYTIKDGFNLKGANLSTNFNGQNTEINSRNFTRLLEHHHHHH

来源 Source

来源生物 organism	CLOSTRIDIUM BOTULINUM
NCBI Class编号 ncbi_taxonomy_id	1491
宿主生物 host_organism	ESCHERICHIA COLI

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	768

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1e1h.1
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	d1e1h.2
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 (6 domains)

Domain ID domain_id	1e1hA00
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	1e1hB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	540 —

Domain ID domain_id	1e1hB02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1280 — Metalloproteases ("zincins"), catalytic domain fold
Homologous superfamily homologous superfamily	10 — Clostridium neurotoxins

Domain ID domain_id	1e1hC00
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	1e1hD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	540 —

Domain ID domain_id	1e1hD02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1280 — Metalloproteases ("zincins"), catalytic domain fold
Homologous superfamily homologous superfamily	10 — Clostridium neurotoxins

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8. Citations (1)

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Unit-cell length a length_a	58.064 Å
Unit-cell length b length_b	94.263 Å
Unit-cell length c length_c	100.156 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.52 °
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	1.800 Å
Low-resolution limit resolution_low	19.340 Å
R factor r_factor	—
R_work r_work	0.1960
R_free r_free	0.2370

fit	/app/data/saxs_computation/e1/1e1h/1e1h.fit
pddf	/app/data/pr_computation/e1/1e1h/1e1h.pr.out
profile	/app/data/saxs_computation/e1/1e1h/1e1h.dat

Crystal Structure of recombinant Botulinum Neurotoxin Type A Light Chain, self-inhibiting Zn endopeptidase.

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

BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)