+Open data
-Basic information
Entry | Database: PDB / ID: 8pm3 | ||||||
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Title | Crystal structure of MAP2K6 with a covalent compound GCL94 | ||||||
Components | Dual specificity mitogen-activated protein kinase kinase 6 | ||||||
Keywords | TRANSFERASE / Kinase / Covalent / inhibitor / MAP2K6 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information cellular response to sorbitol / ovulation cycle process / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / mitogen-activated protein kinase kinase / positive regulation of prostaglandin secretion / stress-activated protein kinase signaling cascade / negative regulation of cold-induced thermogenesis / Myogenesis / PI5P Regulates TP53 Acetylation / p38MAPK cascade ...cellular response to sorbitol / ovulation cycle process / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / mitogen-activated protein kinase kinase / positive regulation of prostaglandin secretion / stress-activated protein kinase signaling cascade / negative regulation of cold-induced thermogenesis / Myogenesis / PI5P Regulates TP53 Acetylation / p38MAPK cascade / positive regulation of nitric-oxide synthase biosynthetic process / MAP kinase kinase activity / Uptake and function of anthrax toxins / signal transduction in response to DNA damage / cardiac muscle contraction / stress-activated MAPK cascade / bone development / regulation of signal transduction by p53 class mediator / response to ischemia / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / PKR-mediated signaling / Interleukin-1 signaling / osteoblast differentiation / cellular senescence / MAPK cascade / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / positive regulation of MAPK cascade / cytoskeleton / regulation of cell cycle / positive regulation of apoptotic process / response to xenobiotic stimulus / positive regulation of protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein kinase binding / signal transduction / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wang, G.Q. / Seidler, N. / Roehm, S. / Gehringer, M. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Crystal structure of MAP2K6 with a covalent compound GCL94 Authors: Wang, G.Q. / Seidler, N. / Roehm, S. / Gehringer, M. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pm3.cif.gz | 231.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pm3.ent.gz | 184.6 KB | Display | PDB format |
PDBx/mmJSON format | 8pm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pm3_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8pm3_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8pm3_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 8pm3_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/8pm3 ftp://data.pdbj.org/pub/pdb/validation_reports/pm/8pm3 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 32749.885 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: LIG is a covalent compound / Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K6, MEK6, MKK6, PRKMK6, SKK3 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P52564, mitogen-activated protein kinase kinase #2: Chemical | ChemComp-ZLE / ~{ #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.57 Å3/Da / Density % sol: 52.09 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05M magnesium chloride -- 30% PEG500MME -- 0.1M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.62 Å / Num. obs: 88885 / % possible obs: 98.9 % / Redundancy: 5.8 % / CC1/2: 0.99 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2→2.04 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4551 / CC1/2: 0.88 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.921 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.296 Å2
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Refinement step | Cycle: 1 / Resolution: 2→48.62 Å
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