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1yxw

A common binding site for disialyllactose and a tri-peptide in the C-fragment of tetanus neurotoxin

Method: X-RAY DIFFRACTION Dmax: 84.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tetanus toxin (Tentoxylysin)

OrganismNot specified

UniProt P04958

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 874–1314 Not recorded TYR TYROSINE × 1 GLU GLUTAMIC ACID × 1 TRP TRYPTOPHAN × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 4000, imidazol, MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.20 Å R-free 0.274

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 1YXW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A8D TETANUS TOXIN C FRAGMENT Deposited 1998-03-23 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 864–1314（451 aa） Fragment：C-FRAGMENT
Mutation：INS(M1) AU GOLD ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions fiber seeding using cryshed initial crystals as seeds；pH 7；9% (W/V) 1M AMMONIUM PHOSPHATE, PH 6.0, AND 92% OF A 10% (W/V) SOLUTION OF PEG 6000 IN 50MM HEPES (PH 7.0). LARGE CRYSTALS (0.2 X 0.2 X 0.5 MM) WERE GROWN BY FIBER SEEDING, USING CRUSHED INITIAL CRYSTALS AS SEEDS., fiber seeding using cryshed initial crystals as seeds
Resolution 1.57 Å R-free 0.262
1AF9 TETANUS NEUROTOXIN C FRAGMENT Deposited 1997-03-24 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 864–1314（451 aa） Fragment：C FRAGMENT
Mutation：MET INSERTED AT N-TERMINUS No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；CRYSTALLIZATION DROP CONTAINED 3 PARTS RESERVOIR SOLUTION AND 1 PART PROTEIN SOLUTION. RESERVOIR: 14%- 18% PEG 4000, 0.1M IMIDAZOLE, 0.05M MGCL2 AT PH 6.5. PROTEIN SOLUTION: 10MG/ML PROTEIN AND 0.01M TRIS-HCL AT PH 7.8.
Resolution 2.70 Å R-free 0.245
1D0H THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH N-ACETYL-GALACTOSAMINE Deposited 1999-09-10 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 872–1315（444 aa） Fragment：C-TERMINAL DOMAIN OF HEAVY CHAIN
Mutation：ADDITION OF THE SEQUENCE MGHGHHHHHHHHHHSSGHIEGRHML AT THE N-TERMINAL RESIDUE 872 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.00
Resolution 2.10 Å R-free 0.270
1DFQ THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH SIALIC ACID Deposited 1999-11-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 871–1314（444 aa） Fragment：C-TERMINAL DOMAIN OF HEAVY CHAIN
Not recorded SLB N-acetyl-beta-neuraminic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；IMIDAZOLE, SODIUM CHLORIDE, AMMONIUM SULFATE, PEG4000, 2-METHYL-2,4-PENTANE-DIOL, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.60 Å R-free 0.313
1DIW THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH GALACTOSE Deposited 1999-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 874–1314（441 aa）
Not recorded GAL beta-D-galactopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；IMIDAZOLE, SODIUM CHLORIDE, AMMONIUM SULPHATE, PEG4000, 2-METHYL-2,4-PENTANE- DIOL, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.00 Å R-free 0.267
1DLL The HC fragement of tetanus toxin complexed with lactose Deposited 1999-12-10 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 874–1314（441 aa） Fragment：RECEPTOR BINDING FRAGMENT HC
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；imidazole, sodium chloride, ammonium sulphate, PEG4000, 2-methyl-2,4-pentane-diol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.80 Å R-free 0.267
1FV2 The Hc fragment of tetanus toxin complexed with an analogue of its ganglioside receptor GT1B Deposited 2000-09-18 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 864–1314（451 aa） Fragment：C-TERMINAL DOMAIN OF HEAVY CHAIN
Not recorded PO4 PHOSPHATE ION × 1 CEQ ETHYL-TRIMETHYL-SILANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% Polyethylene glycol 8000, sodium-potassium phosphate, TRIS, imidazole, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.50 Å R-free 0.276
1FV3 THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH AN ANALOGUE OF ITS GANGLIOSIDE RECEPTOR GT1B Deposited 2000-09-18 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 864–1314（451 aa） Fragment：C-TERMINAL DOMAIN OF HEAVY CHAIN
Not recorded CEQ ETHYL-TRIMETHYL-SILANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；20% Polyethylene glycol 8000, sodium-potassium phosphate, TRIS, imidazole, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.306
1FV3 THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH AN ANALOGUE OF ITS GANGLIOSIDE RECEPTOR GT1B Deposited 2000-09-18 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 864–1314（451 aa） Fragment：C-TERMINAL DOMAIN OF HEAVY CHAIN
Not recorded CEQ ETHYL-TRIMETHYL-SILANE × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；20% Polyethylene glycol 8000, sodium-potassium phosphate, TRIS, imidazole, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.306
1YVG Structural analysis of the catalytic domain of tetanus neurotoxin Deposited 2005-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–457（457 aa） Fragment：chain L
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG 4000, magnesium chloride, hepes buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.276
1YVG Structural analysis of the catalytic domain of tetanus neurotoxin Deposited 2005-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–457（457 aa） Fragment：chain L
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG 4000, magnesium chloride, hepes buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.276
1YYN A common binding site for disialyllactose and a tri-peptide in the C-fragment of tetanus neurotoxin Deposited 2005-02-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 874–1314（441 aa） Fragment：residues 875-1315
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 4000, imidazol, MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.288
1Z7H 2.3 Angstrom crystal structure of tetanus neurotoxin light chain Deposited 2005-03-24 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 0–442（443 aa）
Mutation：I361V ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 3350, MAGNESIUM NITRATE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Resolution 2.30 Å R-free 0.216
3HMY Crystal structure of HCR/T complexed with GT2 Deposited 2009-05-29 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 866–1315（450 aa） Fragment：Receptor binding domain (UNP residues 866-1315)
Not recorded GOL GLYCEROL × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；Bis-Tis propane buffer pH 7.0, 25% PEG2K and 300 mM Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.00 Å R-free 0.237
3HN1 Crystal structure of HCR/T complexed with GT2 and lactose Deposited 2009-05-29 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 866–1315（450 aa） Fragment：Receptor binding domain (UNP residues 866-1315)
Not recorded GLA alpha-D-galactopyranose × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；Bis-Tris propane, PEG2K and ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.10 Å R-free 0.257
4J1L Mutant Endotoxin TeNT Deposited 2013-02-01 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 2–427（426 aa） Fragment：UNP residues 2-427
Mutation：K168E, L230I ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.266
5N0B Crystal structure of the tetanus neurotoxin in complex with GD1a Deposited 2017-02-02 Different construct Different mutation/modification 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 1–1315（1315 aa）
Mutation：R372A, Y375F ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% v/v polyethylene glycol 3350, 0.1M Bis-Tris propane pH 6.5, 0.2M potassium thiocyanate
Resolution 2.60 Å R-free 0.247
5N0C Crystal structure of the tetanus neurotoxin in complex with GM1a Deposited 2017-02-02 Different construct Different mutation/modification 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 1–1315（1315 aa）
Mutation：R372A, Y375F ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；20% v/v polyethylene glycol 6000, 0.1M MES pH 6.0, 0.2M sodium chloride
Resolution 2.60 Å R-free 0.253
5N0C Crystal structure of the tetanus neurotoxin in complex with GM1a Deposited 2017-02-02 Different construct Different mutation/modification 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 1–1315（1315 aa）
Mutation：R372A, Y375F ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；20% v/v polyethylene glycol 6000, 0.1M MES pH 6.0, 0.2M sodium chloride
Resolution 2.60 Å R-free 0.253
7BXX Tetanus neurotoxin translocation domain -C467S Deposited 2020-04-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 459–864（406 aa）
Mutation：C467S No recorded non-water small molecule Experimental method not declared
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；0.225M MES/Bis-Tris pH 6.6, 6.6% PEG6000
Resolution 2.34 Å R-free 0.253
7BXX Tetanus neurotoxin translocation domain -C467S Deposited 2020-04-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 459–864（406 aa）
Mutation：C467S No recorded non-water small molecule Experimental method not declared
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；0.225M MES/Bis-Tris pH 6.6, 6.6% PEG6000
Resolution 2.34 Å R-free 0.253
7BY4 Tetanus neurotoxin receptor binding domain Deposited 2020-04-21 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 865–1315（451 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 NA SODIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0, 0.1 M Pottasium chloride 22.5% PEG 4000
Resolution 1.50 Å R-free 0.163
7BY5 Tetanus neurotoxin mutant-(H233A/E234Q/H237A/Y375F) Deposited 2020-04-21 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 2–1315（1314 aa）
Mutation：H233A,E234Q,H237A,Y375F EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 8 NA SODIUM ION × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M MOPS pH 7.0, 9% PEG 8000
Resolution 2.27 Å R-free 0.233
9FYQ Cryo-EM structure of native SV2A in complex with TeNT-Hc, gangliosides and Pro-Macrobody 5 Deposited 2024-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 875–1315（441 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 6UZ omega-undecylenyl-beta-D-maltopyranoside × 1 A1IHM (2~{R},4~{R},5~{S},6~{S})-2-[(2~{R},3~{R})-3-[(2~{R},3~{S},4~{S},6~{S})-6-[(2~{S},3~{S},4~{R},5~{S},6~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-(hydroxymethyl)-6-[(2~{R},3~{R},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[2-(octadecanoylamino)-3-oxidanyl-octadec-4-enoxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-5-oxidanyl-oxan-4-yl]oxy-3-azanyl-6-carboxy-4-oxidanyl-oxan-2-yl]-2,3-bis(oxidanyl)propoxy]-5-azanyl-4-oxidanyl-6-[(1~{R},2~{S})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid × 1 A1IHN (2~{S},4~{S},5~{R},6~{S})-5-acetamido-2-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-[(2~{R},3~{R},4~{S},5~{R},6~{S})-2-[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(2~{S},4~{S},5~{S},6~{S})-5-acetamido-2-carboxy-4-oxidanyl-6-[(1~{S},2~{R})-1,2,3-tris(oxidanyl)propyl]oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-6-[2-(docosanoylamino)-3-oxidanyl-octadec-4-enoxy]-2-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]oxy-2-(hydroxymethyl)-5-oxidanyl-oxan-3-yl]oxy-6-(hydroxymethyl)-5-oxidanyl-3-(2-oxidanylidenepropyl)oxan-4-yl]oxy-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl]oxy-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM Hepes-NaOH 7.5, 150 mM NaCl, 3 mM maltose, 0.03 % n-dodecyl-beta-D-maltopyranoside, 0.006% cholesterol hemisuccinate
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9FYR Cryo-EM structure of native SV2A in complex with TeNT-Hc, Pro-Macrobody 5 and Levetiracetam Deposited 2024-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 875–1315（441 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 6UZ omega-undecylenyl-beta-D-maltopyranoside × 1 UKX (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM Hepes-NaOH 7.5, 150 mM NaCl, 3 mM maltose, 0.03 % n-dodecyl-beta-D-maltopyranoside, 0.006% cholesterol hemisuccinate, 250 uM Levetiracetam
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å

21 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TETX_CLOTE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–441； UniProt 874–1314

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 1yxw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1yxw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1yxw
Deposition date deposition_date2005-02-22
Structure title titleA common binding site for disialyllactose and a tri-peptide in the C-fragment of tetanus neurotoxin
Keywords keywordsTetanus toxin, GD3, Ganglioside, beta-trefoil, inhibitors, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.66 Å
Radius of gyration Rg (electron density) rg_electron24.63 Å
Forward intensity I(0) i041332300.00
Molecular weight molecular_weight50920.0 kDa
Excluded volume excluded_volume64165 ų
Envelope volume envelope_volume75485 ų
Hydration-shell volume shell_volume26160 ų
Envelope diameter envelope_diameter87.4 Å
Shell Rg shell_rg31.30 Å
Envelope Rg envelope_rg24.82 Å
Shape Rg shape_rg24.60 Å
Total Rg total_rg25.51 Å
Total atoms total_atoms3600
Residues n_residues441
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 dmax84.8 Å
Rg (real space) rg_real25.73 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real4.1330e+07
I(0) uncertainty (real space) i0_real_error6.4190e+05
Rg (reciprocal space) rg_reciprocal25.71 Å
I(0) (reciprocal space) i0_reciprocal41330000.0000
Solution quality estimate total_estimate0.8788
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.3 Å
Skewness Skewness skewness0.445
Kurtosis Kurtosis kurtosis-0.309
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7315000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.946
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1yxwa1
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_idd1yxwa2
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

CATH v4.4 (2 domains)

Domain ID domain_id1yxwA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id1yxwA02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
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8. Citations (1)

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9. Files and Curves (10)