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1pwu

Crystal Structure of Anthrax Lethal Factor complexed with (3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-Trp-methylamide), a known small molecule inhibitor of matrix metalloproteases.

Method: X-RAY DIFFRACTION Dmax: 118.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lethal factor

Bacillus anthracis

UniProt P15917

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 34–809 Mutation：E720C ZN ZINC ION × 1 GM6 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulfate, Tris-HCl, EDTA., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å R-free 0.270
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 34–809 Mutation：E720C ZN ZINC ION × 1 GM6 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulfate, Tris-HCl, EDTA., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å R-free 0.270

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 1PWU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1J7N Anthrax Toxin Lethal factor Deposited 2001-05-17 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 34–809（776 aa）
Chain B 34–809（776 aa）
Not recorded SO4 SULFATE ION × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；ammonium sulfate, TRIS, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.261
1JKY Crystal Structure of the Anthrax Lethal Factor (LF): Wild-type LF Complexed with the N-terminal Sequence of MAPKK2 Deposited 2001-07-13 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 34–809（776 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；1.9M Ammonium sulfate, 0.2M Tris pH 8.0, 2mM EDTA
Resolution 3.90 Å R-free 0.316
1PWP Crystal Structure of the Anthrax Lethal Factor complexed with Small Molecule Inhibitor NSC 12155 Deposited 2003-07-02 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 34–809（776 aa）
Not recorded ZN ZINC ION × 1 NSC N,N'-BIS(4-AMINO-2-METHYLQUINOLIN-6-YL)UREA × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulfate, Tris-HCl, EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.274
1PWP Crystal Structure of the Anthrax Lethal Factor complexed with Small Molecule Inhibitor NSC 12155 Deposited 2003-07-02 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 34–809（776 aa）
Not recorded ZN ZINC ION × 1 NSC N,N'-BIS(4-AMINO-2-METHYLQUINOLIN-6-YL)UREA × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulfate, Tris-HCl, EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.274
1PWQ Crystal structure of Anthrax Lethal Factor complexed with Thioacetyl-Tyr-Pro-Met-Amide, a metal-chelating peptidyl small molecule inhibitor Deposited 2003-07-02 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 34–809（776 aa）
Not recorded ZN ZINC ION × 1 SD2 N-(SULFANYLACETYL)TYROSYLPROLYLMETHIONINAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulfate, Tris-HCl, EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.52 Å R-free 0.311
1PWQ Crystal structure of Anthrax Lethal Factor complexed with Thioacetyl-Tyr-Pro-Met-Amide, a metal-chelating peptidyl small molecule inhibitor Deposited 2003-07-02 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 34–809（776 aa）
Not recorded ZN ZINC ION × 1 SD2 N-(SULFANYLACETYL)TYROSYLPROLYLMETHIONINAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulfate, Tris-HCl, EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.52 Å R-free 0.311
1PWV Crystal structure of Anthrax Lethal Factor wild-type protein complexed with an optimised peptide substrate. Deposited 2003-07-02 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 34–809（776 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulphate, Tris-HCl, EDTA., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.85 Å R-free 0.279
1PWV Crystal structure of Anthrax Lethal Factor wild-type protein complexed with an optimised peptide substrate. Deposited 2003-07-02 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 B 34–809（776 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulphate, Tris-HCl, EDTA., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.85 Å R-free 0.279
1PWV Crystal structure of Anthrax Lethal Factor wild-type protein complexed with an optimised peptide substrate. Deposited 2003-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 34–809（776 aa）
Chain B 34–809（776 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulphate, Tris-HCl, EDTA., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.85 Å R-free 0.279
1PWW Crystal structure of Anthrax Lethal Factor active site mutant protein complexed with an optimised peptide substrate in the presence of zinc. Deposited 2003-07-02 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 34–809（776 aa）
Mutation：E687C ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulphate, Tris-HCl, EDTA. , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.288
1PWW Crystal structure of Anthrax Lethal Factor active site mutant protein complexed with an optimised peptide substrate in the presence of zinc. Deposited 2003-07-02 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 B 34–809（776 aa）
Mutation：E687C ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulphate, Tris-HCl, EDTA. , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.288
1PWW Crystal structure of Anthrax Lethal Factor active site mutant protein complexed with an optimised peptide substrate in the presence of zinc. Deposited 2003-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 34–809（776 aa）
Chain B 34–809（776 aa）
Mutation：E687C Mutation：E687C ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Ammonium sulphate, Tris-HCl, EDTA. , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.288
1YQY Structure of B. Anthrax Lethal factor in complex with a hydroxamate inhibitor Deposited 2005-02-02 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 297–809（513 aa） Fragment：domains II-IV (residues 297-809)
Not recorded ZN ZINC ION × 1 915 (2R)-2-{[(4-FLUORO-3-METHYLPHENYL)SULFONYL]AMINO}-N-HYDROXY-2-TETRAHYDRO-2H-PYRAN-4-YLACETAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；Peg 8K, magnesium acetate, Sodium cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.269
2L0R Conformational Dynamics of the Anthrax Lethal Factor Catalytic Center Deposited 2010-07-15 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 705–809（105 aa） Fragment：C-terminal 106 residues catalytic core domain (Domain IV), UNP residues 705-809
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) Pi 50；Pressure ambient
NMR sample composition 0.6 mM [U-99% 13C; U-99% 15N] Anthrax LF C-term-1, 10 % % [U-99% 2H] D2O-2, 90 % % H2O-3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3KWV Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers Deposited 2009-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 34–296（263 aa） Fragment：protective antigen binding domain (UNP residues 34-296)
Not recorded CA CALCIUM ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；16% PEG 3000, 0.1M cacodylic acid, 0.2M magnesium chloride, 10 mM Tris-Cl, 75 mM sodium chloride, 10 mM adenosine-5'-triphosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.281
3KWV Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers Deposited 2009-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 34–296（263 aa） Fragment：protective antigen binding domain (UNP residues 34-296)
Not recorded CA CALCIUM ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；16% PEG 3000, 0.1M cacodylic acid, 0.2M magnesium chloride, 10 mM Tris-Cl, 75 mM sodium chloride, 10 mM adenosine-5'-triphosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.281
4DV8 Anthrax Lethal Factor metalloproteinase in complex with the Hydroxamic acid based small molecule PT8421 Deposited 2012-02-22 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 296–809（514 aa）
Not recorded ZN ZINC ION × 1 0LX (2S)-6-[(4-fluorobenzyl)amino]-2-[(2R)-2-(4-fluorophenyl)-2-methoxyethyl]-N-hydroxyhexanamide × 1 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；0.03M citric acid, 0.01M BIS-Tris, Propane, pH7.6, 20% PEG3350, 14 mg/mL protein, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.63 Å R-free 0.204
4PKQ Anthrax toxin lethal factor with bound zinc Deposited 2014-05-15 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 298–809（512 aa） Fragment：UNP residues 298-809
Mutation：A266S ZN ZINC ION × 1 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.20 Å R-free 0.217
4PKR Anthrax toxin lethal factor with bound small molecule inhibitor 10 Deposited 2014-05-15 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 298–809（512 aa） Fragment：UNP residues 298-809
Mutation：A266S 2ZL N~2~-benzyl-N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-D-alaninamide × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.20 Å R-free 0.253
4PKS Anthrax toxin lethal factor with bound small molecule inhibitor 11 Deposited 2014-05-15 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 298–809（512 aa） Fragment：UNP residues 298-809
Mutation：A266S ZN ZINC ION × 1 30H N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-N~2~-(pyridin-3-ylmethyl)-D-alaninamide × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.30 Å R-free 0.260
4PKT Anthrax toxin lethal factor with bound small molecule inhibitor 13 Deposited 2014-05-15 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 298–809（512 aa） Fragment：UNP residues 298-809
Mutation：A266S 30O N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-N~2~-(4-nitrobenzyl)-D-alaninamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.40 Å R-free 0.240
4PKU Anthrax toxin lethal factor with bound small molecule inhibitor 15 Deposited 2014-05-15 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 298–809（512 aa） Fragment：UNP residues 298-809
Mutation：A266S 30P N~2~-(3-aminobenzyl)-N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-D-alaninamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.40 Å R-free 0.249
4PKV Anthrax toxin lethal factor with bound small molecule inhibitor 16 Deposited 2014-05-15 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 298–809（512 aa） Fragment：UNP residues 298-809
Mutation：A266S 30R N~2~-[4-(aminomethyl)benzyl]-N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-D-alaninamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.50 Å R-free 0.253
4PKW Anthrax toxin lethal factor with bound small molecule inhibitor GM6001 Deposited 2014-05-15 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 298–809（512 aa） Fragment：UNP residues 298-809
Mutation：A266S ZN ZINC ION × 1 GM6 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 1.75 Å R-free 0.207
4WF6 Anthrax toxin lethal factor with bound small molecule inhibitor MK-31 Deposited 2014-09-12 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 298–809（512 aa） Fragment：UNP residues 298-809
Mutation：A266S ZN ZINC ION × 1 407 N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-D-alaninamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.65 Å R-free 0.240
4XM6 Anthrax toxin lethal factor with ligand-induced binding pocket Deposited 2015-01-14 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 298–809（512 aa） Fragment：UNP residues 298-809
Mutation：A266S 41R N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-N~2~-(2-methylpropyl)-D-valinamide × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.35 Å R-free 0.246
4XM7 Anthrax toxin lethal factor with ligand-induced binding pocket Deposited 2015-01-14 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 298–809（512 aa） Fragment：UNP residues 298-809
Mutation：A266S 41S N~2~-[(4-fluoro-3-methoxyphenyl)sulfonyl]-N-hydroxy-N~2~-(2-methylpropyl)-D-valinamide × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.70 Å R-free 0.269
4XM8 Anthrax toxin lethal factor with ligand-induced binding pocket Deposited 2015-01-14 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 298–809（512 aa） Fragment：UNP residues 298-809
Mutation：A266S 41T N-hydroxy-N~2~-{[3-(methoxymethyl)phenyl]sulfonyl}-N~2~-(2-methylpropyl)-D-valinamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.70 Å R-free 0.276
5D1S Anthrax toxin lethal factor with hydroxamic acid inhibitor Deposited 2015-08-04 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 298–809（512 aa） Fragment：residues 298-809
Mutation：A299S 56Q N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-N~2~-methyl-D-alaninamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.10 Å R-free 0.247
5D1T Anthrax toxin lethal factor with hydroxamic acid inhibitor Deposited 2015-08-04 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 298–809（512 aa） Fragment：residues 298-809
Mutation：A299S ZN ZINC ION × 1 56R N~2~-[3-(aminomethyl)benzyl]-N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-D-alaninamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.20 Å R-free 0.255
5D1U Anthrax toxin lethal factor with hydroxamic acid inhibitor Deposited 2015-08-04 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 298–809（512 aa） Fragment：residues 298-809
Mutation：A299S 56P N~2~-(6-aminohexyl)-N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-D-alaninamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；286 K；11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate
Resolution 2.85 Å R-free 0.252
6PSN Anthrax toxin protective antigen channels bound to lethal factor Deposited 2019-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain L 1–809（809 aa）
Not recorded CA CALCIUM ION × 14 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6ZXJ Fully-loaded anthrax lethal toxin in its heptameric pre-pore state, in which the third lethal factor is masked out (PA7LF3-masked) Deposited 2020-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 1–809（809 aa）
Chain I 1–809（809 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE；4 uL sample was applied to grid (with 2 nm additional carbon layer) and incubated for 45 s prior blotting.
Resolution 3.50 Å
6ZXK Fully-loaded anthrax lethal toxin in its heptameric pre-pore state and PA7LF(2+1B) arrangement Deposited 2020-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain H 1–809（809 aa）
Chain I 1–809（809 aa）
Chain J 1–809（809 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE；4 uL sample was applied to grid (with 2 nm additional carbon layer) and incubated for 45 s prior blotting.
Resolution 3.80 Å
6ZXL Fully-loaded anthrax lethal toxin in its heptameric pre-pore state and PA7LF(2+1A) arrangement Deposited 2020-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain H 1–809（809 aa）
Chain I 1–809（809 aa）
Chain J 1–809（809 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE；4 uL sample was applied to grid (with 2 nm additional carbon layer) and incubated for 45 s prior blotting.
Resolution 4.20 Å
7KXR Protective antigen pore translocating lethal factor N-terminal domain Deposited 2020-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain L 34–296（263 aa） Fragment：UNP Residues 34-296
Mutation：E126C CA CALCIUM ION × 14 ELECTRON MICROSCOPY
cryo-EM buffer pH 5.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8FVU Cryo-EM structure of human Needle/NAIP/NLRC4 (R288A) Deposited 2023-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain U 34–296（263 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å

30 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LEF_BACAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–776； UniProt 34–809 Author chain B； PDBConstruct 1–776； UniProt 34–809

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 1pwu

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1pwu
Deposition date deposition_date2003-07-02
Structure title titleCrystal Structure of Anthrax Lethal Factor complexed with (3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-Trp-methylamide), a known small molecule inhibitor of matrix metalloproteases.
Keywords keywordsAnthrax Toxin, Lethal Factor, small molecule peptidic inhibitor, hydroxamic acid., 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_guinier38.43 Å
Radius of gyration Rg (electron density) rg_electron37.74 Å
Forward intensity I(0) i0439778000.00
Molecular weight molecular_weight173340.0 kDa
Excluded volume excluded_volume218240 ų
Envelope volume envelope_volume296950 ų
Hydration-shell volume shell_volume64376 ų
Envelope diameter envelope_diameter122.2 Å
Shell Rg shell_rg44.91 Å
Envelope Rg envelope_rg36.95 Å
Shape Rg shape_rg37.74 Å
Total Rg total_rg38.18 Å
Total atoms total_atoms12238
Residues n_residues1483
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 dmax118.0 Å
Rg (real space) rg_real38.17 Å
Rg uncertainty (real space) rg_real_error0.92 Å
I(0) (real space) i0_real4.3980e+08
I(0) uncertainty (real space) i0_real_error7.6050e+06
Rg (reciprocal space) rg_reciprocal38.33 Å
I(0) (reciprocal space) i0_reciprocal439800000.0000
Solution quality estimate total_estimate0.8979
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.8 Å
Skewness Skewness skewness0.111
Kurtosis Kurtosis kurtosis-0.509
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha97750000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.885
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1pwua1
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.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains
Domain ID domain_idd1pwua2
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.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains
Domain ID domain_idd1pwua3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.166 — ADP-ribosylation
Superfamily Superfamily superfamilyd.166.1 — ADP-ribosylation
Family Family familyd.166.1.1 — ADP-ribosylating toxins
Domain ID domain_idd1pwub1
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.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains
Domain ID domain_idd1pwub2
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.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains
Domain ID domain_idd1pwub3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.166 — ADP-ribosylation
Superfamily Superfamily superfamilyd.166.1 — ADP-ribosylation
Family Family familyd.166.1.1 — ADP-ribosylating toxins

CATH v4.4 (8 domains)

Domain ID domain_id1pwuA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1pwuA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Domain ID domain_id1pwuA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2030 — Anthrax toxin lethal factor, domain 3, chain A
Homologous superfamily homologous superfamily10 — Anthrax toxin lethal factor, domain 3, chain A
Domain ID domain_id1pwuA04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1pwuB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1pwuB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Domain ID domain_id1pwuB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2030 — Anthrax toxin lethal factor, domain 3, chain A
Homologous superfamily homologous superfamily10 — Anthrax toxin lethal factor, domain 3, chain A
Domain ID domain_id1pwuB04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
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8. Citations (1)

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9. Files and Curves (10)