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2nyy

Crystal structure of botulinum neurotoxin type A complexed with monoclonal antibody CR1

Method: X-RAY DIFFRACTION Dmax: 180.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Botulinum neurotoxin type A

OrganismNot specified

UniProt P10845

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–1295 Not recorded CR1 monoclonal antibody × 1 CR1 monoclonal antibody × 1 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

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 2NYY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2NZ9 Crystal structure of botulinum neurotoxin type A complexed with monoclonal antibody AR2 Deposited 2006-11-22 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1295（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 oligomeric state 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） 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 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：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 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：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 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：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 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：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 oligomeric state 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 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 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 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）
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 construct Different oligomeric state Different ligand/ion 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 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） 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 construct 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 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
5MK7 Crystal structure of the receptor-binding domain of botulinum neurotoxin A1 (crystal form 2) Deposited 2016-12-02 Different construct 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 871–1296（426 aa）
Not recorded No recorded non-water small molecule 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
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 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 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）
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 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
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 oligomeric state 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 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 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 oligomeric state 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 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
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 oligomeric state 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 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）
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 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）
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 1–1295； UniProt 1–1295

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 2nyy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2nyy
Deposition date deposition_date2006-11-21
Structure title titleCrystal structure of botulinum neurotoxin type A complexed with monoclonal antibody CR1
Keywords keywordsBOTULINUM, NEUROTOXIN, FAB, PROTEIN ANTIBODY COMPLEX, TOXIN-IMMUNE SYSTEM COMPLEX; TOXIN/IMMUNE SYSTEM
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_guinier49.42 Å
Radius of gyration Rg (electron density) rg_electron49.96 Å
Forward intensity I(0) i0520680000.00
Molecular weight molecular_weight191360.0 kDa
Excluded volume excluded_volume240280 ų
Envelope volume envelope_volume325670 ų
Hydration-shell volume shell_volume58084 ų
Envelope diameter envelope_diameter185.6 Å
Shell Rg shell_rg48.47 Å
Envelope Rg envelope_rg50.26 Å
Shape Rg shape_rg49.93 Å
Total Rg total_rg50.00 Å
Total atoms total_atoms13507
Residues n_residues1700
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 dmax180.8 Å
Rg (real space) rg_real50.11 Å
Rg uncertainty (real space) rg_real_error1.95 Å
I(0) (real space) i0_real5.2070e+08
I(0) uncertainty (real space) i0_real_error1.0390e+07
Rg (reciprocal space) rg_reciprocal49.42 Å
I(0) (reciprocal space) i0_reciprocal520200000.0000
Solution quality estimate total_estimate0.7982
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.2 Å
Skewness Skewness skewness0.572
Kurtosis Kurtosis kurtosis-0.176
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha41120000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.694; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.697; Smooth: 0.594
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd2nyya1
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_idd2nyya2
Class classh — Coiled coil proteins
Fold Fold foldh.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamilyh.4.2 — Clostridium neurotoxins, 'coiled-coil' domain
Family Family familyh.4.2.1 — Clostridium neurotoxins, 'coiled-coil' domain
Domain ID domain_idd2nyya3
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.6 — Clostridium neurotoxins, the second last domain
Domain ID domain_idd2nyya4
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.4 — STI-like
Family Family familyb.42.4.2 — Clostridium neurotoxins, C-terminal domain
Domain ID domain_idd2nyyc1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd2nyyc2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2nyyd1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2nyyd2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2nyyd3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id2nyyA01
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_id2nyyA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1120 — Clostridium botulinum neurotoxin B, "coiled-coil" domain
Homologous superfamily homologous superfamily10 — Clostridium botulinum neurotoxin b, "coiled-coil" domain
Domain ID domain_id2nyyA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id2nyyA04
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
Domain ID domain_id2nyyC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2nyyC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2nyyD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2nyyD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)