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2g7k

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

Method: X-RAY DIFFRACTION Dmax: 108.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Botulinum neurotoxin type A

Clostridium botulinum

UniProt Q45894

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 No other associated polymer 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
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 No other associated polymer 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

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 2G7K 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
2G7N Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to small Molecule Inhibitors Deposited 2006-02-28 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 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
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 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
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 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
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 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
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 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 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.

SAXS scattering curve SAXS Profile

SAXS profile for 2g7k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2g7k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2g7k
Deposition date deposition_date2006-02-28
Structure title titleStructure of the Light Chain of Botulinum Neurotoxin, Serotype A Bound to small Molecule Inhibitors
Keywords keywordsBotulinum neurotoxin, zinc protease, SNAP25, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.11 Å
Radius of gyration Rg (electron density) rg_electron32.77 Å
Forward intensity I(0) i0124724000.00
Molecular weight molecular_weight91616.0 kDa
Excluded volume excluded_volume115540 ų
Envelope volume envelope_volume142030 ų
Hydration-shell volume shell_volume37054 ų
Envelope diameter envelope_diameter117.4 Å
Shell Rg shell_rg38.43 Å
Envelope Rg envelope_rg32.71 Å
Shape Rg shape_rg32.72 Å
Total Rg total_rg33.38 Å
Total atoms total_atoms6481
Residues n_residues800
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax108.8 Å
Rg (real space) rg_real33.26 Å
Rg uncertainty (real space) rg_real_error0.89 Å
I(0) (real space) i0_real1.2470e+08
I(0) uncertainty (real space) i0_real_error2.0390e+06
Rg (reciprocal space) rg_reciprocal33.20 Å
I(0) (reciprocal space) i0_reciprocal124700000.0000
Solution quality estimate total_estimate0.8803
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.7 Å
Skewness Skewness skewness0.390
Kurtosis Kurtosis kurtosis-0.530
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27420000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.910
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2g7ka_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.7 — Clostridium neurotoxins, catalytic domain
Domain ID domain_idd2g7kb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.7 — Clostridium neurotoxins, catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id2g7kA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1240 — Zincin-like
Homologous superfamily homologous superfamily10 — Metalloproteases ("zincins"), catalytic domain like
Domain ID domain_id2g7kB00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1240 — Zincin-like
Homologous superfamily homologous superfamily10 — Metalloproteases ("zincins"), catalytic domain like
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8. Citations (1)

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9. Files and Curves (10)