+Open data
-Basic information
Entry | Database: PDB / ID: 4bf2 | ||||||
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Title | Crystal Structures of Ask1-inhibitor Complexes | ||||||
Components | MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress ...cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of cardiac muscle cell apoptotic process / p38MAPK cascade / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / MAP kinase kinase kinase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of protein kinase activity / positive regulation of myoblast differentiation / stress-activated MAPK cascade / positive regulation of JUN kinase activity / JNK cascade / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to amino acid starvation / response to endoplasmic reticulum stress / response to ischemia / apoptotic signaling pathway / positive regulation of JNK cascade / cellular response to hydrogen peroxide / MAPK cascade / cellular senescence / cellular response to tumor necrosis factor / protein phosphatase binding / Oxidative Stress Induced Senescence / neuron apoptotic process / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / external side of plasma membrane / protein phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Singh, O. / Shillings, A. / Craggs, P. / Wall, I. / Rowland, P. / Skarzynski, T. / Hobbs, C.I. / Hardwick, P. / Tanner, R. / Blunt, M. ...Singh, O. / Shillings, A. / Craggs, P. / Wall, I. / Rowland, P. / Skarzynski, T. / Hobbs, C.I. / Hardwick, P. / Tanner, R. / Blunt, M. / Witty, D.R. / Smith, K.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2013 Title: Crystal Structures of Ask1-Inhibtor Complexes Provide a Platform for Structure Based Drug Design. Authors: Singh, O. / Shillings, A. / Craggs, P. / Wall, I. / Rowland, P. / Skarzynski, T. / Hobbs, C.I. / Hardwick, P. / Tanner, R. / Blunt, M. / Witty, D.R. / Smith, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bf2.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bf2.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/4bf2 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bf2 | HTTPS FTP |
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-Related structure data
Related structure data | 4bhnC 4bibC 4bicC 4bidC 4bieC 2clqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37518.453 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 660-977 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q99683, mitogen-activated protein kinase kinase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.43 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 18% PEG 3.4K, 0.2M NA ACETATE, 0.1M BIS-TRIS BUFFER PH 6.5, 0.2% ISOPROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→40 Å / Num. obs: 42333 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.11→2.15 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.2 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CLQ Resolution: 2.11→13.36 Å / Cor.coef. Fo:Fc: 0.9405 / Cor.coef. Fo:Fc free: 0.9142 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.168
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Displacement parameters | Biso mean: 53.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→13.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.17 Å / Total num. of bins used: 20
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