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- PDB-4wf6: Anthrax toxin lethal factor with bound small molecule inhibitor MK-31 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wf6 | ||||||||||||
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Title | Anthrax toxin lethal factor with bound small molecule inhibitor MK-31 | ||||||||||||
![]() | Lethal factor | ||||||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Anthrax toxin / lethal factor / metalloproteinase / metalloprotease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||||||||
Function / homology | ![]() anthrax lethal factor endopeptidase / host cell cytosol / Uptake and function of anthrax toxins / metalloendopeptidase activity / metallopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Maize, K.M. / De la Mora-Rey, T. / Finzel, B.C. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Probing the S2' Subsite of the Anthrax Toxin Lethal Factor Using Novel N-Alkylated Hydroxamates. Authors: Kurbanov, E.K. / Chiu, T.L. / Solberg, J. / Francis, S. / Maize, K.M. / Fernandez, J. / Johnson, R.L. / Hawkinson, J.E. / Walters, M.A. / Finzel, B.C. / Amin, E.A. #1: Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: The discovery of a potent and selective lethal factor inhibitor for adjunct therapy of anthrax infection. Authors: Xiong, Y. / Wiltsie, J. / Woods, A. / Guo, J. / Pivnichny, J.V. / Tang, W. / Bansal, A. / Cummings, R.T. / Cunningham, B.R. / Friedlander, A.M. / Douglas, C.M. / Salowe, S.P. / Zaller, D.M. ...Authors: Xiong, Y. / Wiltsie, J. / Woods, A. / Guo, J. / Pivnichny, J.V. / Tang, W. / Bansal, A. / Cummings, R.T. / Cunningham, B.R. / Friedlander, A.M. / Douglas, C.M. / Salowe, S.P. / Zaller, D.M. / Scolnick, E.M. / Schmatz, D.M. / Bartizal, K. / Hermes, J.D. / MacCoss, M. / Chapman, K.T. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.9 KB | Display | ![]() |
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PDB format | ![]() | 89.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5d1sC ![]() 5d1tC ![]() 5d1uC ![]() 1yqyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 60436.047 Da / Num. of mol.: 1 / Fragment: UNP residues 298-809 / Mutation: A266S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P15917, anthrax lethal factor endopeptidase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-407 / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.37 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 13, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.64→50 Å / Num. obs: 17862 / % possible obs: 99 % / Redundancy: 5.4 % / Biso Wilson estimate: 35.01 Å2 / Rmerge(I) obs: 0.106 / Χ2: 0.248 / Net I/av σ(I): 6.962 / Net I/σ(I): 3.8 / Num. measured all: 95814 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YQY Resolution: 2.6521→32.487 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.59 Å2 / Biso mean: 37.5265 Å2 / Biso min: 12.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6521→32.487 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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