+Open data
-Basic information
Entry | Database: PDB / ID: 5j95 | ||||||
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Title | MAP4K4 in complex with inhibitor | ||||||
Components | Mitogen-activated protein kinase kinase kinase kinase 4 | ||||||
Keywords | Transferase/Transferase Inhibitor / kinase / inhibitor complex / structural based drug design / Transferase-Transferase Inhibitor complex | ||||||
Function / homology | Function and homology information positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity ...positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity / MAPK cascade / microtubule binding / Oxidative Stress Induced Senescence / non-specific serine/threonine protein kinase / positive regulation of cell migration / intracellular signal transduction / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Liu, S. | ||||||
Citation | Journal: To Be Published Title: MAP4K4 in complex with inhibitor Authors: Liu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j95.cif.gz | 249.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j95.ent.gz | 201.6 KB | Display | PDB format |
PDBx/mmJSON format | 5j95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/5j95 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/5j95 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35733.059 Da / Num. of mol.: 2 / Fragment: UNP residues 2-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K4, HGK, KIAA0687, NIK Production host: Insect cell expression vector pTIE1 (others) References: UniProt: O95819, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-6HH / | #3: 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: 2.49 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH=6.5, 0.2 M NaCl, 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→96.4 Å / Num. obs: 25413 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 75.38 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.5→2.8 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.137 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→66.66 Å / Cor.coef. Fo:Fc: 0.9326 / Cor.coef. Fo:Fc free: 0.9015 / SU R Cruickshank DPI: 0.469 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.45 / SU Rfree Blow DPI: 0.273 / SU Rfree Cruickshank DPI: 0.279
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Displacement parameters | Biso mean: 77.06 Å2
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Refine analyze | Luzzati coordinate error obs: 0.415 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.5→66.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.6 Å / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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