SAXSdb — 3k3q

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

Botulinum neurotoxin type A

Clostridium botulinum A str. Hall

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain B； UniProt 3–250 Chain C； UniProt 251–425	Fragment：N-terminal fragment of BoNT catalytic domain (residues 3-250) Fragment：C-terminal fragment of BoNT catalytic domain (residues 251-425)	llama Aa1 VHH domain × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；25% ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.256
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 3–250 Chain C； UniProt 251–425	Fragment：N-terminal fragment of BoNT catalytic domain (residues 3-250) Fragment：C-terminal fragment of BoNT catalytic domain (residues 251-425)	llama Aa1 VHH domain × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；25% ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.256

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 3K3Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2W2D Crystal Structure of a Catalytically Active, Non-toxic Endopeptidase Derivative of Clostridium botulinum Toxin A Deposited 2008-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–442（442 aa） Fragment：RESIDUES 1-442 Chain B 447–877（431 aa） Fragment：RESIDUES 447-877	Not recorded	SO4 SULFATE ION × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PROTEIN: 0.05 M HEPES PH 7.2 AND 0.2 M NACL MOTHER LIQUOR: 15% SUCROSE, 0.1 M TRIS PH 8.5, 1.5 M AMMONIUM SULPHATE.	Resolution 2.59 Å R-free 0.253
2W2D Crystal Structure of a Catalytically Active, Non-toxic Endopeptidase Derivative of Clostridium botulinum Toxin A Deposited 2008-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–442（442 aa） Fragment：RESIDUES 1-442 Chain D 447–877（431 aa） Fragment：RESIDUES 447-877	Not recorded	SO4 SULFATE ION × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PROTEIN: 0.05 M HEPES PH 7.2 AND 0.2 M NACL MOTHER LIQUOR: 15% SUCROSE, 0.1 M TRIS PH 8.5, 1.5 M AMMONIUM SULPHATE.	Resolution 2.59 Å R-free 0.253
3BWI Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with an acetate ion bound at the active site Deposited 2008-01-09	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 1–424（424 aa） Fragment：residues 1-424	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；15% PEG 3350, 0.3M ammonium sulfate, 0.1M Bis-Tris , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.70 Å R-free 0.240
3C88 Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with inhibitory peptide RRGC Deposited 2008-02-11	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 1–424（424 aa） Fragment：residues 1-424	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；12% PEG 3350, 0.2M ammonium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.217
3C89 Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with inhibitory peptide RRGM Deposited 2008-02-11	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 1–424（424 aa） Fragment：RESIDUES 1-424	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；15% PEG 3350, 0.3M AMMONIUM SULFATE, 0.1M BIS-TRIS, pH 6.40, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.58 Å R-free 0.208
3C8A Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with inhibitory peptide RRGL Deposited 2008-02-11	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 1–424（424 aa） Fragment：RESIDUES 1-424	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；293 K；18% PEG 3350, 0.3M AMMONIUM SULFATE, 0.1M BIS-TRIS, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.52 Å R-free 0.207
3C8B Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with inhibitory peptide RRGI Deposited 2008-02-11	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 1–424（424 aa） Fragment：RESIDUES 1-424	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；293 K；17% PEG 3350, 0.25M AMMONIUM SULFATE, 0.1M BIS-TRIS, pH 6.90, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.47 Å R-free 0.216
3DDA Crystal structure of the catalytic domain of Botulinum neurotoxin serotype a with a snap-25 peptide Deposited 2008-06-05	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 1–424（424 aa） Fragment：residues 1-424	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% PEG8000, 0.2M Ammoium Sulfate, 0.1M Sodium Cacodylate, 5% Ethylene Glycol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.50 Å R-free 0.200
3DDB Crystal structure of the catalytic domain of Botulinum neurotoxin serotype a with a substrate analog peptide Deposited 2008-06-05	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 1–424（424 aa） Fragment：residues 1-424	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% PEG8000, 0.2M Ammoium Sulfate, 0.1M Sodium Cacodylate, 5% Ethylene Glycol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.218
3DS9 A potent peptidomimetic inhibitor of botulinum neurotoxin serotype A has a very different conformation than SNAP-25 substrate Deposited 2008-07-11	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 1–417（417 aa） Fragment：light chain	Mutation：residues 2-420	ZN ZINC ION × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.1X PEG MME 2000, 5 mM NiCl2, and 100 mM HEPES pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.76 Å R-free 0.248
3DSE A potent peptidomimetic inhibitor of botulinum neurotoxin serotype A has a very different conformation than SNAP-25 substrate Deposited 2008-07-11	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 1–417（417 aa） Fragment：light chain	Mutation：residues 2-420	ZN ZINC ION × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.1X PEG MME 2000, 5 mM NiCl2, and 100 mM HEPES pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.243
3QIX Crystal Structure of BoNT/A LC with Zinc bound Deposited 2011-01-28	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 3–424（422 aa） Fragment：light chain (UNP residues 3-424)	Not recorded	EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG6000, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.41 Å R-free 0.228
3QIX Crystal Structure of BoNT/A LC with Zinc bound Deposited 2011-01-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 3–424（422 aa） Fragment：light chain (UNP residues 3-424)	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG6000, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.41 Å R-free 0.228
3QIY Crystal Structure of BoNT/A LC complexed with Hydroxamate-based Inhibitor PT-1 Deposited 2011-01-28	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 3–424（422 aa） Fragment：light chain (UNP residues 3-424)	Not recorded	ZN ZINC ION × 1 QI1 4-[bis(4-chlorobenzyl)amino]-N-hydroxybutanamide × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；293 K；13% PEG6000, 100 mM MES, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.263
3QIZ Crystal Structure of BoNT/A LC complexed with Hydroxamate-based Inhibitor PT-2 Deposited 2011-01-28	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 3–424（422 aa） Fragment：light chain (UNP residues 3-424)	Not recorded	ZN ZINC ION × 1 QI2 (2S,4R)-2-(2-{[3-(4-fluoro-3-methylphenyl)propyl](methyl)amino}ethyl)-4-(4-fluorophenyl)-N-hydroxy-4-methoxybutanamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG6000, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.223
3QJ0 Crystal Structure of BoNT/A LC complexed with Hydroxamate-based Inhibitor PT-3 Deposited 2011-01-28	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 3–424（422 aa） Fragment：light chain (UNP residues 3-424)	Not recorded	ZN ZINC ION × 1 QI3 (4R)-4-(4-chlorophenoxy)-1-[(4-chlorophenyl)sulfonyl]-N-hydroxy-L-prolinamide × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% PEG6000, 100 mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.229
3QW5 Crystal structure of the protease domain of Botulinum Neurotoxin Serotype A with a peptide inhibitor RRGF Deposited 2011-02-26	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 1–424（424 aa） Fragment：light chain (UNP residues 1-424)	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；25% PEG3350, 0.3 M ammonium sulfate, pH 6.60, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.232
3QW6 Crystal structure of the protease domain of Botulinum Neurotoxin Serotype A with a peptide inhibitor RYGC Deposited 2011-02-26	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 1–424（424 aa） Fragment：light chain (UNP residues 1-424)	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；293 K；22% PEG3350, 0.3 M ammonium sulfate, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.222
3QW7 Crystal structure of the protease domain of Botulinum Neurotoxin Serotype A with a peptide inhibitor RRFC Deposited 2011-02-27	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 1–424（424 aa） Fragment：light chain (UNP residues 1-424)	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；293 K；22% PEG3350, 0.3 M ammonium sulfate, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.50 Å R-free 0.209
3QW8 Crystal structure of the protease domain of Botulinum Neurotoxin Serotype A with a peptide inhibitor CRGC Deposited 2011-02-27	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 1–424（424 aa） Fragment：light chain (UNP residues 1-424)	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；22% PEG3350, 0.3 M ammonium sulfate, pH 6.80, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.217
4KS6 Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S mutant with covalent inhibitor that modifies Cys-165 causing disorder in 166-174 stretch Deposited 2013-05-17	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 1–425（425 aa） Fragment：Catalytic domain residues 1-425	Mutation：C134S	ZN ZINC ION × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 PGO S-1,2-PROPANEDIOL × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；protein complex - 6 microL LCA C134S at 145 microM + 1.4 microL KG23 at 1.25 milli-M, Reservoir - 17.5% PEG 600, 0.065 M HEPES pH 7.5. Cryoprotectant - CryoProtX CM1, 10% PEG 20K, 100 milliM CHC (citric acid, HEPES, CHES - 40% pH 4 / 60% pH 10), VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.93 Å R-free 0.252
4KTX Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S mutant with covalent inhibitor that modifies Cys-165 causing disorder in 167-174 stretch Deposited 2013-05-21	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 1–425（425 aa） Fragment：Catalytic domain residues 1-425	Mutation：C134S	ZN ZINC ION × 1 PGO S-1,2-PROPANEDIOL × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；293 K；Protein - preformed complex LCA_C134S-KG13 at 10 mg/mL, Reservoir - 4% PEG 4000, 0.1 M imidazole malate, Cryoprotectant 40% CryoProtX CM3, 18% MPEG 2K, 0.1 M PCTP (Na propionate, Na cacodylate, Bis-Tris-propane) (50% pH 4 / 50% pH 9.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.59 Å R-free 0.298
4KUF Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134 mutant with MTSEA modified Cys-165 causing stretch disorder Deposited 2013-05-22	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 1–425（425 aa） Fragment：Catalytic domain residues 1-425	Mutation：C134S Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 DMS DIMETHYL SULFOXIDE × 4 LMR (2S)-2-hydroxybutanedioic acid × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 9 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；LCA-C134S-MTSEA at 3 mg/ml in 0.010 M Tris-HCl, pH 7.9, 0.050 M Li2SO4, DROPS - 3+3 micro-l, RESERVOIR - 42% MPEG-550, 0.1 M Li2SO4, 0.2 M imidazole malate, pH 5.5, CRYOSOLUTION - 18% MPEG2K, 22% MPD, 10% DMSO, 0.050 M bicine, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.70 Å R-free 0.231
5L21 Crystal structure of BoNT/A receptor binding domain in complex with VHH C2 Deposited 2016-07-29	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 872–1296（425 aa）	Mutation：T1158A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；18% polyethylene glycol 6,000; 100 mM Sodium Acetate, pH 5.0	Resolution 1.68 Å R-free 0.205

22 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BXA1_CLOBH
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain B； PDBConstruct 5–252； UniProt 3–250 Author chain C； PDBConstruct 1–175； UniProt 251–425

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	3k3q
Deposition date deposition_date	2009-10-04
Structure title title	Crystal Structure of a Llama Antibody complexed with the C. Botulinum Neurotoxin Serotype A Catalytic Domain
Keywords keywords	;llama, VHH, antibody, botulinum, neurotoxin, BoNT, Cell junction, Cell membrane, Cytoplasm, Disulfide bond, Hydrolase, Membrane, Metal-binding, Metalloprotease, Pharmaceutical, Protease, Secreted, Synapse, Toxin, Transmembrane, Zinc, IMMUNE SYSTEM ;; IMMUNE SYSTEM
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	26.06 Å
Radius of gyration Rg (electron density) rg_electron	24.93 Å
Forward intensity I(0) i0	59802800.00
Molecular weight molecular_weight	60771.0 kDa
Excluded volume excluded_volume	76256 Å³
Envelope volume envelope_volume	92990 Å³
Hydration-shell volume shell_volume	30827 Å³
Envelope diameter envelope_diameter	89.6 Å
Shell Rg shell_rg	32.32 Å
Envelope Rg envelope_rg	25.15 Å
Shape Rg shape_rg	24.89 Å
Total Rg total_rg	25.89 Å
Total atoms total_atoms	4288
Residues n_residues	540
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	87.7 Å
Rg (real space) rg_real	25.97 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	5.9800e+07
I(0) uncertainty (real space) i0_real_error	8.4500e+05
Rg (reciprocal space) rg_reciprocal	26.00 Å
I(0) (reciprocal space) i0_reciprocal	59800000.0000
Solution quality estimate total_estimate	0.6766
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.1 Å
Skewness Skewness skewness	0.243
Kurtosis Kurtosis kurtosis	-0.353
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	14850000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 0.105; Positv: 1.000; Valcen: 0.999; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	llama Aa1 VHH domain
Molecular weight formula_weight	16147.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4358

MDIAVQLVDSGGGTLQAGKSLRLSCAISGLAFDGGAMGSEHRLTAGAMGWFRQAPGKDREFVAAISPRTDETYYAESLEGRFSVSRDAAATMVFLQADNVRLDDTASYYCAADEDVTPRVMGVIPHADHWGQGTLVTVSSAAALEHHHHHH

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Botulinum neurotoxin type A
Molecular weight formula_weight	28360.0 kDa
EC 编号 ec_number	3.4.24.69
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAVQFVNKQFNYKDPVNGVDIAYIKIPNVGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAY

来源 Source

来源生物 organism	Clostridium botulinum A str. Hall
NCBI Class编号 ncbi_taxonomy_id	441771
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Botulinum neurotoxin type A
Molecular weight formula_weight	20621.5 kDa
EC 编号 ec_number	3.4.24.69
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

YEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLFEF

来源 Source

来源生物 organism	Clostridium botulinum A str. Hall
NCBI Class编号 ncbi_taxonomy_id	441771
宿主生物 host_organism	Escherichia coli

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	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	70

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3k3qa_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3k3qA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3k3qB00
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	3k3qC01
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	3k3qC02
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	168.282 Å
Unit-cell length b length_b	48.764 Å
Unit-cell length c length_c	103.643 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.2180
R_free r_free	0.2560

fit	/app/data/saxs_computation/k3/3k3q/3k3q.fit
pddf	/app/data/pr_computation/k3/3k3q/3k3q.pr.out
profile	/app/data/saxs_computation/k3/3k3q/3k3q.dat

Crystal Structure of a Llama Antibody complexed with the C. Botulinum Neurotoxin Serotype A Catalytic Domain

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)