5mk7

Crystal structure of the receptor-binding domain of botulinum neurotoxin A1 (crystal form 2)

Method: X-RAY DIFFRACTION D_max: 82.2 Å Quality: GOOD

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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 871–1296	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；289.15 K；0.1 M MIB, 25% w/v PEG 1500	Resolution 1.80 Å R-free 0.223

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 5MK7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NYY Crystal structure of botulinum neurotoxin type A complexed with monoclonal antibody CR1 Deposited 2006-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1295（1295 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；297 K；8% PEG 20000, 8% PEG 550 MME, 200 mM calcium acetate, 100 mM sodium acetate, pH 5.50, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.61 Å R-free 0.246
2NZ9 Crystal structure of botulinum neurotoxin type A complexed with monoclonal antibody AR2 Deposited 2006-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1295（1295 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；297 K；8% PEG 20000, 8% PEG 550 MME, 200 mM calcium acetate, 100 mM sodium acetate, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 3.79 Å R-free 0.278
2NZ9 Crystal structure of botulinum neurotoxin type A complexed with monoclonal antibody AR2 Deposited 2006-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–1295（1295 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；297 K；8% PEG 20000, 8% PEG 550 MME, 200 mM calcium acetate, 100 mM sodium acetate, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 3.79 Å R-free 0.278
2VU9 CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE A BINDING DOMAIN IN COMPLEX WITH GT1B Deposited 2008-05-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 876–1296（421 aa） Fragment：BINDING DOMAIN, RESIDUES 876-1296	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；21% PEG3350, 0.2 M MGCL2, 0.1 M BISTRIS PH5.5	Resolution 1.60 Å R-free 0.186
2VUA Crystal Structure of the Botulinum Neurotoxin Serotype A binding domain Deposited 2008-05-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 876–1296（421 aa） Fragment：BINDING DOMAIN, RESIDUES 876-1296	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.2；18% PEG3350, 0.2 M MGCL2, 0.1 M BISTRIS PH 5.2	Resolution 1.70 Å R-free 0.205
3BTA CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE A Deposited 1998-08-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1295（1295 aa） Fragment：FULL LENGTH TOXIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 3.20 Å R-free 0.280
3FUO The Crystal structure of receptor binding domain of botulinum neurotoxin serotype A Deposited 2009-01-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 871–1296（426 aa） Fragment：sequence database residues 871-1296	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；292 K；0.1 M Hepes pH 7.6, 12% PEG8K, 8% glycerol and 0.1 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.80 Å R-free 0.248
3ZUR Crystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC0-A-SNAP25-Hn-A Deposited 2011-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–431（429 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 3-431, SNAP25, RESIDUES 145-206, TRANSLOCATION DOMAIN RESIDUES, 454-865 Chain A 454–865（412 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 3-431, SNAP25, RESIDUES 145-206, TRANSLOCATION DOMAIN RESIDUES, 454-865	Mutation：YES Mutation：YES	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M TRIS PH 7.5, 0.2 M LISO4, 15% PEG 3350.	Resolution 2.71 Å R-free 0.266
3ZUR Crystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC0-A-SNAP25-Hn-A Deposited 2011-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 3–431（429 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 3-431, SNAP25, RESIDUES 145-206, TRANSLOCATION DOMAIN RESIDUES, 454-865 Chain B 454–865（412 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 3-431, SNAP25, RESIDUES 145-206, TRANSLOCATION DOMAIN RESIDUES, 454-865	Mutation：YES Mutation：YES	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M TRIS PH 7.5, 0.2 M LISO4, 15% PEG 3350.	Resolution 2.71 Å R-free 0.266
3ZUS Crystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC-A-SNAP23-Hn-A Deposited 2011-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–431（429 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865 Chain A 454–865（412 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M IMIDAZOLE MALATE PH 6.0, 15% PEG 3350.	Resolution 2.95 Å R-free 0.293
3ZUS Crystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC-A-SNAP23-Hn-A Deposited 2011-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 3–431（429 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865 Chain B 454–865（412 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M IMIDAZOLE MALATE PH 6.0, 15% PEG 3350.	Resolution 2.95 Å R-free 0.293
3ZUS Crystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC-A-SNAP23-Hn-A Deposited 2011-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 3–431（429 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865 Chain C 454–865（412 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M IMIDAZOLE MALATE PH 6.0, 15% PEG 3350.	Resolution 2.95 Å R-free 0.293
3ZUS Crystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC-A-SNAP23-Hn-A Deposited 2011-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 3–431（429 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865 Chain D 454–865（412 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M IMIDAZOLE MALATE PH 6.0, 15% PEG 3350.	Resolution 2.95 Å R-free 0.293
4EJ5 Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A wild-type Deposited 2012-04-06	Different construct 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：UNP residues 1-425	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 1 IMD IMIDAZOLE × 1 CO3 CARBONATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；8.3% monomethyl polyethylene glycol 2000, 0.17 M lithium sulfate, 6.25% 4,2 methyl pentane diol, 0.1 M imidazole malate, pH 6.0, cryoprotectant: 18% MPEG2K, 22% MPD, 10% DMSO, .050 M bicine, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.87 Å R-free 0.208
4EL4 Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S/C165S double mutant Deposited 2012-04-10	Different construct 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 1–425（425 aa） Fragment：UNP residues 1-425	Mutation：C134S, C165S	ZN ZINC ION × 1 GOL GLYCEROL × 2 IMD IMIDAZOLE × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；reservoir: 29% MPEG2K, 0.04 M Li2SO4, 0.1 M imidazole-HCl pH 6.0, cryoprotectant: 18% MPEG2K, 22% MPD, 10% DMSO, 0.050 M bicine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.20 Å R-free 0.202
4ELC Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134 mutant with MTSEA modified Cys-165 Deposited 2012-04-10	Different construct 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 1–425（425 aa） Fragment：UNP residues 1-425	Mutation：C134S Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 IMD IMIDAZOLE × 2 LMR (2S)-2-hydroxybutanedioic acid × 1 DMS DIMETHYL SULFOXIDE × 3 SO4 SULFATE ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 LI LITHIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.223
4HEV Clostridium Botulinum Serotype A Light Chain Inhibited By Adamantane Hydroxamate Deposited 2012-10-04	Different construct 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：UNP Residues 1-425	Not recorded	ZN ZINC ION × 1 AXM N-hydroxy-2-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；10-12mg/ml enzyme in 50mM NaPO4, 2mM EDTA, pH 6.5; and 10-15% polyethylene glycol (PEG) 2,000 monomethyl ester, 0.2-0.3M K2HPO4, 0.1M D,L-malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.248
4HEV Clostridium Botulinum Serotype A Light Chain Inhibited By Adamantane Hydroxamate Deposited 2012-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–425（425 aa） Fragment：UNP Residues 1-425	Not recorded	ZN ZINC ION × 1 AXM N-hydroxy-2-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；10-12mg/ml enzyme in 50mM NaPO4, 2mM EDTA, pH 6.5; and 10-15% polyethylene glycol (PEG) 2,000 monomethyl ester, 0.2-0.3M K2HPO4, 0.1M D,L-malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.248
4IQP Crystal Structure of HCRA-W1266A Deposited 2013-01-12	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 871–1296（426 aa）	Mutation：W1266A	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；292 K；0.1 M Hepes, 12% PEG3350, 100 mM NaCl, pH 7.5, EVAPORATION, temperature 292K	Resolution 2.30 Å R-free 0.246
4JRA CRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING DOMAIN IN COMPLEX WITH THE LUMINAL DOMAIN Of SV2C Deposited 2013-03-21	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）	Not recorded	CL CHLORIDE ION × 6 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；100 mM Hepes pH 7.5, 6% PEG 8000, 8% Glycerol, 100 mM NaCl, VAPOR DIFFUSION, temperature 293K	Resolution 2.30 Å R-free 0.269
4JRA CRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING DOMAIN IN COMPLEX WITH THE LUMINAL DOMAIN Of SV2C Deposited 2013-03-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 871–1296（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；100 mM Hepes pH 7.5, 6% PEG 8000, 8% Glycerol, 100 mM NaCl, VAPOR DIFFUSION, temperature 293K	Resolution 2.30 Å R-free 0.269
4ZJX Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with a Novel Cyclic Peptide Inhibitor Deposited 2015-04-29	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 1–424（424 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG 3350, BIs-Tris and Lithium Sulfate	Resolution 1.94 Å R-free 0.229
5JLV Receptor binding domain of Botulinum neurotoxin A in complex with human glycosylated SV2C Deposited 2016-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 872–1296（425 aa） Fragment：UNP residues 872-1296	Mutation：T1158A	ACT ACETATE ION × 1 PO4 PHOSPHATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium acetate pH 4.6, 20% PEG 3350, 0.2 M ammonium phosphate monobasic, 4% polypropylene glycol P 400	Resolution 2.00 Å R-free 0.216
5JLV Receptor binding domain of Botulinum neurotoxin A in complex with human glycosylated SV2C Deposited 2016-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 872–1296（425 aa） Fragment：UNP residues 872-1296	Mutation：T1158A	ACT ACETATE ION × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium acetate pH 4.6, 20% PEG 3350, 0.2 M ammonium phosphate monobasic, 4% polypropylene glycol P 400	Resolution 2.00 Å R-free 0.216
5JMC Receptor binding domain of Botulinum neurotoxin A in complex with rat SV2C Deposited 2016-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 872–1296（425 aa） Fragment：UNP residues 872-1296	Mutation：A1158T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM sodium cacodylate, pH 6.5, 13% polyethylene glycol (PEG) 3350, 200 mM NaCl	Resolution 2.64 Å R-free 0.275
5JMC Receptor binding domain of Botulinum neurotoxin A in complex with rat SV2C Deposited 2016-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 872–1296（425 aa） Fragment：UNP residues 872-1296	Mutation：A1158T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM sodium cacodylate, pH 6.5, 13% polyethylene glycol (PEG) 3350, 200 mM NaCl	Resolution 2.64 Å R-free 0.275
5JMC Receptor binding domain of Botulinum neurotoxin A in complex with rat SV2C Deposited 2016-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 872–1296（425 aa） Fragment：UNP residues 872-1296	Mutation：A1158T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM sodium cacodylate, pH 6.5, 13% polyethylene glycol (PEG) 3350, 200 mM NaCl	Resolution 2.64 Å R-free 0.275
5JMC Receptor binding domain of Botulinum neurotoxin A in complex with rat SV2C Deposited 2016-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 872–1296（425 aa） Fragment：UNP residues 872-1296	Mutation：A1158T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM sodium cacodylate, pH 6.5, 13% polyethylene glycol (PEG) 3350, 200 mM NaCl	Resolution 2.64 Å R-free 0.275
5MK6 Crystal structure of the receptor-binding domain of botulinum neurotoxin A1 (crystal form 1) Deposited 2016-12-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 871–1296（426 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；289.15 K；0.1 M MIB, 25% w/v PEG 1500	Resolution 1.45 Å R-free 0.221
5TPB Binding domain of BoNT/A complexed with ganglioside variant Deposited 2016-10-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 876–1296（421 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% PEG3350, 0.2 M potassium thiocyanate, 0.1 M BisTris propane pH 6.5	Resolution 2.60 Å R-free 0.240
5TPB Binding domain of BoNT/A complexed with ganglioside variant Deposited 2016-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 876–1296（421 aa）	Not recorded	SIA N-acetyl-alpha-neuraminic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% PEG3350, 0.2 M potassium thiocyanate, 0.1 M BisTris propane pH 6.5	Resolution 2.60 Å R-free 0.240
5TPC Binding domain of BoNT/A complexed with ganglioside Deposited 2016-10-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 876–1296（421 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% PEG6000, 0.2 M MgCl2, 0.1 M Hepes pH 7.0	Resolution 2.00 Å R-free 0.238
5V8P Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain Deposited 2017-03-22	Different construct 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 1–424（424 aa） Fragment：residues 1-424	Mutation：P2Q	ZN ZINC ION × 1 90G N-[3-(4-chlorophenyl)-1H-pyrazol-5-yl]-2-sulfanylacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Equal volumes of 10-12 mg/ml enzyme (50 mM Na2HPO4, 2 mM EDTA, pH 6.5) and crystallization buffer (10-15% polyethylene glycol [PEG] 2,000 monomethyl ester, 0.2-0.3 M K2HPO4, 0.1 M D,L-malic acid pH 7.0)	Resolution 2.50 Å R-free 0.252
5V8P Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain Deposited 2017-03-22	Different construct 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 1–424（424 aa） Fragment：residues 1-424	Mutation：P2Q	ZN ZINC ION × 1 90G N-[3-(4-chlorophenyl)-1H-pyrazol-5-yl]-2-sulfanylacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Equal volumes of 10-12 mg/ml enzyme (50 mM Na2HPO4, 2 mM EDTA, pH 6.5) and crystallization buffer (10-15% polyethylene glycol [PEG] 2,000 monomethyl ester, 0.2-0.3 M K2HPO4, 0.1 M D,L-malic acid pH 7.0)	Resolution 2.50 Å R-free 0.252
5V8R Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain Deposited 2017-03-22	Different construct 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 90J N-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]-2-sulfanylacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；Mix equal volumes of 10 mg/ml enzyme (20 mM HEPES, pH 7.5, 50 mM NaCl) with crystallization solution (10%-15% polyethylene glycol monomethyl ether 2000, 0.3 M (NH4)2HPO4, 50 mM Tris, pH 8.5)	Resolution 1.90 Å R-free 0.222
5V8R Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain Deposited 2017-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–424（424 aa） Fragment：residues 1-424	Not recorded	ZN ZINC ION × 1 90J N-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]-2-sulfanylacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；Mix equal volumes of 10 mg/ml enzyme (20 mM HEPES, pH 7.5, 50 mM NaCl) with crystallization solution (10%-15% polyethylene glycol monomethyl ether 2000, 0.3 M (NH4)2HPO4, 50 mM Tris, pH 8.5)	Resolution 1.90 Å R-free 0.222
5V8U Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain Deposited 2017-03-22	Different construct 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 1–424（424 aa） Fragment：residues 1-424	Mutation：P2Q	ZN ZINC ION × 1 90M N-[3-(4-fluorophenyl)-4-methyl-1H-pyrazol-5-yl]-2-sulfanylacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Mix equal volumes of 10-12 mg/ml enzyme (50 mM Na2HPO4, 2 mM EDTA, pH 6.5) and crystallization buffer (10-15% polyethylene glycol [PEG] 2,000 monomethyl ester, 0.2-0.3 M K2HPO4, 0.1 M D,L-malic acid pH 7.0)	Resolution 2.05 Å R-free 0.260
5V8U Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain Deposited 2017-03-22	Different construct 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 1–424（424 aa） Fragment：residues 1-424	Mutation：P2Q	ZN ZINC ION × 1 90M N-[3-(4-fluorophenyl)-4-methyl-1H-pyrazol-5-yl]-2-sulfanylacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Mix equal volumes of 10-12 mg/ml enzyme (50 mM Na2HPO4, 2 mM EDTA, pH 6.5) and crystallization buffer (10-15% polyethylene glycol [PEG] 2,000 monomethyl ester, 0.2-0.3 M K2HPO4, 0.1 M D,L-malic acid pH 7.0)	Resolution 2.05 Å R-free 0.260
5VGV Structure of the C. botulinum neurotoxin serotype A with Cu bound Deposited 2017-04-11	Different construct 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）	Not recorded	CU COPPER (II) ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；PEG8000 6%, Calcium Acetate 0.1 M, Sodium Cacodylate 0.1 M	Resolution 2.60 Å R-free 0.252
5VGX Structure of the C. botulinum neurotoxin serotype A with Hg bound Deposited 2017-04-11	Different construct 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）	Not recorded	HG MERCURY (II) ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；PEG8000 8%, Calcium Acetate 0.2 M, Sodium Cacodylate 0.1 M	Resolution 2.15 Å R-free 0.246
6DKK Structure of BoNT Deposited 2018-05-29	Different construct Different mutation/modification 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 547–871（325 aa） Chain B 547–871（325 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；291 K；1.4 M sodium potassium phosphate and 0.1 M potassium sodium tartrate tetrahydrate	Resolution 2.70 Å R-free 0.223

26 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BXA1_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–433； UniProt 871–1296

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5mk7
Deposition date deposition_date	2016-12-02
Structure title title	Crystal structure of the receptor-binding domain of botulinum neurotoxin A1 (crystal form 2)
Keywords keywords	bacterial, toxin, Toxin receptor binding domain, jelly roll fold, beta trefoil fold; TOXIN
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	25.10 Å
Radius of gyration Rg (electron density) rg_electron	23.95 Å
Forward intensity I(0) i0	34954900.00
Molecular weight molecular_weight	46227.0 kDa
Excluded volume excluded_volume	58118 Å³
Envelope volume envelope_volume	69000 Å³
Hydration-shell volume shell_volume	24604 Å³
Envelope diameter envelope_diameter	86.4 Å
Shell Rg shell_rg	30.67 Å
Envelope Rg envelope_rg	24.09 Å
Shape Rg shape_rg	23.90 Å
Total Rg total_rg	24.89 Å
Total atoms total_atoms	3263
Residues n_residues	397
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	82.2 Å
Rg (real space) rg_real	25.17 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	3.4950e+07
I(0) uncertainty (real space) i0_real_error	5.0640e+05
Rg (reciprocal space) rg_reciprocal	25.15 Å
I(0) (reciprocal space) i0_reciprocal	34950000.0000
Solution quality estimate total_estimate	0.8822
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.439
Kurtosis Kurtosis kurtosis	-0.339
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6026000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.958

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Botulinum neurotoxin type A
Molecular weight formula_weight	50711.4 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	A
Atom count atom_count	3585

MHHHHHHKNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGTKFIIKKYASGNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPL

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	322

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5mk7a1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.6 — Clostridium neurotoxins, the second last domain

Domain ID domain_id	d5mk7a2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.4 — STI-like
Family Family family	b.42.4.2 — Clostridium neurotoxins, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	5mk7A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	5mk7A02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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8. Citations (1)

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Unit-cell length a length_a	61.363 Å
Unit-cell length b length_b	53.927 Å
Unit-cell length c length_c	62.687 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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	60.242 Å
R factor r_factor	0.1894
R_work r_work	0.1876
R_free r_free	0.2231

fit	/app/data/saxs_computation/mk/5mk7/5mk7.fit
pddf	/app/data/pr_computation/mk/5mk7/5mk7.pr.out
profile	/app/data/saxs_computation/mk/5mk7/5mk7.dat