SAXSdb — 2g7q

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

Botulinum neurotoxin type A

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–425	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–425	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

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 2G7Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E1H Crystal Structure of recombinant Botulinum Neurotoxin Type A Light Chain, self-inhibiting Zn endopeptidase. Deposited 2000-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 10–250（241 aa） Fragment：RESIDUES 10-250 Chain B 251–416（166 aa） Fragment：RESIDUES 252-416 Chain C 10–250（241 aa） Fragment：RESIDUES 10-250 Chain D 251–416（166 aa） Fragment：RESIDUES 252-416	Mutation：YES 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
2G7K Structure of the Light Chain of Botulinum Neurotoxin, Serotype A Bound to small Molecule Inhibitors Deposited 2006-02-28	Different mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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
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 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BXA2_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–425； UniProt 2–425 Author chain B； PDBConstruct 2–425； UniProt 2–425

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	2g7q
Deposition date deposition_date	2006-02-28
Structure title title	Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule Inhibitors
Keywords keywords	botulinum neurotoxin, zinc protease, SNAP25, 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	32.96 Å
Radius of gyration Rg (electron density) rg_electron	32.60 Å
Forward intensity I(0) i0	132025000.00
Molecular weight molecular_weight	93923.0 kDa
Excluded volume excluded_volume	118300 Å³
Envelope volume envelope_volume	148250 Å³
Hydration-shell volume shell_volume	38685 Å³
Envelope diameter envelope_diameter	117.6 Å
Shell Rg shell_rg	38.58 Å
Envelope Rg envelope_rg	32.59 Å
Shape Rg shape_rg	32.57 Å
Total Rg total_rg	33.22 Å
Total atoms total_atoms	6638
Residues n_residues	820
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	109.5 Å
Rg (real space) rg_real	33.09 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	1.3200e+08
I(0) uncertainty (real space) i0_real_error	2.0490e+06
Rg (reciprocal space) rg_reciprocal	33.04 Å
I(0) (reciprocal space) i0_reciprocal	132000000.0000
Solution quality estimate total_estimate	0.8762
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	107.2 Å
Skewness Skewness skewness	0.396
Kurtosis Kurtosis kurtosis	-0.485
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31550000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.929; Smooth: 0.886

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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
Molecular weight formula_weight	48708.8 kDa
EC 编号 ec_number	3.4.24.69
Mutation mutation	R362A, Y365F
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	6797

MFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHDVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAEHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDVASTLNKAKSIIGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVNFFKVINAKTFLNFDKAVFRINIVPDENYTIKDGFNLKGANLSTNFNGQNTEINSRNFTRLKNFTGLFEFY

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 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	N-HYDROXY-L-ARGININAMIDE
Molecular weight formula_weight	189.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	159

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2g7qA00
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	2g7qB00
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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8. Citations (1)

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Unit-cell length a length_a	69.320 Å
Unit-cell length b length_b	109.940 Å
Unit-cell length c length_c	166.640 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	2.410 Å
Low-resolution limit resolution_low	21.550 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2610

fit	/app/data/saxs_computation/g7/2g7q/2g7q.fit
pddf	/app/data/pr_computation/g7/2g7q/2g7q.pr.out
profile	/app/data/saxs_computation/g7/2g7q/2g7q.dat

Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule Inhibitors

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

Botulinum neurotoxin type A

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