1jky

Crystal Structure of the Anthrax Lethal Factor (LF): Wild-type LF Complexed with the N-terminal Sequence of MAPKK2

Method: X-RAY DIFFRACTION D_max: 111.2 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lethal Factor

Bacillus anthracis

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 34–809	Not recorded	mitogen-activated protein kinase kinase 2 × 1	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

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 1JKY	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
1PWP Crystal Structure of the Anthrax Lethal Factor complexed with Small Molecule Inhibitor NSC 12155 Deposited 2003-07-02	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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
1PWU Crystal Structure of Anthrax Lethal Factor complexed with (3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-Trp-methylamide), a known small molecule inhibitor of matrix metalloproteases. Deposited 2003-07-02	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 34–809（776 aa）	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
1PWU Crystal Structure of Anthrax Lethal Factor complexed with (3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-Trp-methylamide), a known small molecule inhibitor of matrix metalloproteases. Deposited 2003-07-02	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 34–809（776 aa）	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
1PWV Crystal structure of Anthrax Lethal Factor wild-type protein complexed with an optimised peptide substrate. Deposited 2003-07-02	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 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 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 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 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 oligomeric state 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 oligomeric state 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 38 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

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1jky
Deposition date deposition_date	2001-07-13
Structure title title	Crystal Structure of the Anthrax Lethal Factor (LF): Wild-type LF Complexed with the N-terminal Sequence of MAPKK2
Keywords keywords	Lethal Toxin, Mek2, MAPKK, Uncleaved substrate, Protease-substrate complex, TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.79 Å
Radius of gyration Rg (electron density) rg_electron	32.44 Å
Forward intensity I(0) i0	110047000.00
Molecular weight molecular_weight	81041.0 kDa
Excluded volume excluded_volume	100390 Å³
Envelope volume envelope_volume	137480 Å³
Hydration-shell volume shell_volume	36594 Å³
Envelope diameter envelope_diameter	114.9 Å
Shell Rg shell_rg	37.86 Å
Envelope Rg envelope_rg	32.60 Å
Shape Rg shape_rg	32.44 Å
Total Rg total_rg	32.88 Å
Total atoms total_atoms	5734
Residues n_residues	764
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	111.2 Å
Rg (real space) rg_real	32.96 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	1.1000e+08
I(0) uncertainty (real space) i0_real_error	1.6940e+06
Rg (reciprocal space) rg_reciprocal	32.89 Å
I(0) (reciprocal space) i0_reciprocal	110000000.0000
Solution quality estimate total_estimate	0.8688
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.7 Å
Skewness Skewness skewness	0.451
Kurtosis Kurtosis kurtosis	-0.317
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	32410000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.853

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Lethal Factor
Molecular weight formula_weight	90356.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5734

AGGHGDVGMHVKEKEKNKDENKRKDEERNKTQEEHLKEIMKHIVKIEVKGEEAVKKEAAEKLLEKVPSDVLEMYKAIGGKIYIVDGDITKHISLEALSEDKKKIKDIYGKDALLHEHYVYAKEGYEPVLVIQSSEDYVENTEKALNVYYEIGKILSRDILSKINQPYQKFLDVLNTIKNASDSDGQDLLFTNQLKEHPTDFSVEFLEQNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEAFNYMDKFNEQEINLSLEELKDQRMLSRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIRDSLSEEEKELLNRIQVDSSNPLSEKEKEFLKKLKLDIQPYDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHEFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHSTDHAERLKVQKNAPKTFQFINDQIKFIINS

来源 Source

来源生物 organism	Bacillus anthracis
NCBI Class编号 ncbi_taxonomy_id	1392
宿主生物 host_organism	Bacillus anthracis

Entity 2 Entity 2 polymer

Description description	mitogen-activated protein kinase kinase 2
Molecular weight formula_weight	1793.2 kDa
EC 编号 ec_number	2.7.1.-
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MLARRKPVLPALTINP

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1jkya1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains

Domain ID domain_id	d1jkya2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains

Domain ID domain_id	d1jkya3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.1 — ADP-ribosylating toxins

CATH v4.4 (4 domains)

Domain ID domain_id	1jkyA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	1jkyA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	1jkyA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2030 — Anthrax toxin lethal factor, domain 3, chain A
Homologous superfamily homologous superfamily	10 — Anthrax toxin lethal factor, domain 3, chain A

Domain ID domain_id	1jkyA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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8. Citations (1)

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Unit-cell length a length_a	330.700 Å
Unit-cell length b length_b	330.700 Å
Unit-cell length c length_c	330.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	I 41 3 2
Space-group number int_tables_number	214
Crystal system crystal_system	—

Resolution resolution	3.900 Å
Low-resolution limit resolution_low	50.600 Å
R factor r_factor	0.2960
R_work r_work	0.2960
R_free r_free	0.3160

fit	/app/data/saxs_computation/jk/1jky/1jky.fit
pddf	/app/data/pr_computation/jk/1jky/1jky.pr.out
profile	/app/data/saxs_computation/jk/1jky/1jky.dat

Crystal Structure of the Anthrax Lethal Factor (LF): Wild-type LF Complexed with the N-terminal Sequence of MAPKK2

1. Protein Identity and Related Structures Protein Identity & Related Structures

Lethal Factor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)