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3qiz

Crystal Structure of BoNT/A LC complexed with Hydroxamate-based Inhibitor PT-2

Method: X-RAY DIFFRACTION Dmax: 71.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Botulinum neurotoxin type A

Clostridium botulinum

UniProt A5HZZ9

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 3–424 Fragment：light chain (UNP residues 3-424) 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

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 3QIZ 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 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 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 mutation/modification 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 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 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 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 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 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 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 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 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
3K3Q Crystal Structure of a Llama Antibody complexed with the C. Botulinum Neurotoxin Serotype A Catalytic Domain Deposited 2009-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 3–250（248 aa） Fragment：N-terminal fragment of BoNT catalytic domain (residues 3-250)
Chain C 251–425（175 aa） Fragment：C-terminal fragment of BoNT catalytic domain (residues 251-425)
Not recorded 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
3K3Q Crystal Structure of a Llama Antibody complexed with the C. Botulinum Neurotoxin Serotype A Catalytic Domain Deposited 2009-10-04 Different construct Different mutation/modification 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 3–250（248 aa） Fragment：N-terminal fragment of BoNT catalytic domain (residues 3-250)
Chain C 251–425（175 aa） Fragment：C-terminal fragment of BoNT catalytic domain (residues 251-425)
Not recorded 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
3QIX Crystal Structure of BoNT/A LC with Zinc bound Deposited 2011-01-28 Different ligand/ion 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 ligand/ion 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 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
3QJ0 Crystal Structure of BoNT/A LC complexed with Hydroxamate-based Inhibitor PT-3 Deposited 2011-01-28 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 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 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 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 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 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 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BXA1_CLOBH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–424； UniProt 3–424

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 3qiz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3qiz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3qiz
Deposition date deposition_date2011-01-28
Structure title titleCrystal Structure of BoNT/A LC complexed with Hydroxamate-based Inhibitor PT-2
Keywords keywordsBotulinum, BONT, Neurotoxin, Toxin, Hydroxamate, Inhibitor, metalloprotease, protease, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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_guinier22.47 Å
Radius of gyration Rg (electron density) rg_electron21.32 Å
Forward intensity I(0) i033401700.00
Molecular weight molecular_weight46250.0 kDa
Excluded volume excluded_volume58542 ų
Envelope volume envelope_volume67742 ų
Hydration-shell volume shell_volume25807 ų
Envelope diameter envelope_diameter72.8 Å
Shell Rg shell_rg28.68 Å
Envelope Rg envelope_rg21.68 Å
Shape Rg shape_rg21.29 Å
Total Rg total_rg22.32 Å
Total atoms total_atoms3270
Residues n_residues399
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 dmax71.8 Å
Rg (real space) rg_real22.37 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real3.3400e+07
I(0) uncertainty (real space) i0_real_error3.9550e+05
Rg (reciprocal space) rg_reciprocal22.39 Å
I(0) (reciprocal space) i0_reciprocal33400000.0000
Solution quality estimate total_estimate0.7397
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.3 Å
Skewness Skewness skewness0.227
Kurtosis Kurtosis kurtosis-0.358
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9203000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 0.328; Positv: 1.000; Valcen: 0.994; Smooth: 0.994
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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3qiza1
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_idd3qiza2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id3qizA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1240 — Zincin-like
Homologous superfamily homologous superfamily10 — Metalloproteases ("zincins"), catalytic domain like
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8. Citations (1)

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9. Files and Curves (10)