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Yorodumi- PDB-5hes: Human leucine zipper- and sterile alpha motif-containing kinase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hes | ||||||
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Title | Human leucine zipper- and sterile alpha motif-containing kinase (ZAK, MLT, HCCS-4, MRK, AZK, MLTK) in complex with vemurafenib | ||||||
Components | Mitogen-activated protein kinase kinase kinase MLT | ||||||
Keywords | TRANSFERASE / Kinase / Complex | ||||||
Function / homology | Function and homology information positive regulation of mitotic DNA damage checkpoint / negative regulation of stress-activated protein kinase signaling cascade / negative regulation of translation in response to endoplasmic reticulum stress / stalled ribosome sensor activity / GCN2-mediated signaling / cell death / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / positive regulation of programmed cell death / regulation of mitotic metaphase/anaphase transition ...positive regulation of mitotic DNA damage checkpoint / negative regulation of stress-activated protein kinase signaling cascade / negative regulation of translation in response to endoplasmic reticulum stress / stalled ribosome sensor activity / GCN2-mediated signaling / cell death / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / positive regulation of programmed cell death / regulation of mitotic metaphase/anaphase transition / limb development / embryonic digit morphogenesis / cellular response to UV-B / stress-activated protein kinase signaling cascade / protein kinase activator activity / pyroptosis / p38MAPK cascade / MAP kinase kinase kinase activity / stress-activated MAPK cascade / cytoskeleton organization / JNK cascade / DNA damage checkpoint signaling / chromosome segregation / cellular response to gamma radiation / small ribosomal subunit rRNA binding / ribosome binding / protein autophosphorylation / cell differentiation / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Mathea, S. / Salah, E. / Abdul Azeez, K.R. / Tallant, C. / Szklarz, M. / Chaikuad, A. / Shrestha, B. / Sorrell, F.J. / Elkins, J.M. / Shrestha, L. ...Mathea, S. / Salah, E. / Abdul Azeez, K.R. / Tallant, C. / Szklarz, M. / Chaikuad, A. / Shrestha, B. / Sorrell, F.J. / Elkins, J.M. / Shrestha, L. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Structure of the Human Protein Kinase ZAK in Complex with Vemurafenib. Authors: Mathea, S. / Abdul Azeez, K.R. / Salah, E. / Tallant, C. / Wolfreys, F. / Konietzny, R. / Fischer, R. / Lou, H.J. / Brennan, P.E. / Schnapp, G. / Pautsch, A. / Kessler, B.M. / Turk, B.E. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hes.cif.gz | 132 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hes.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 5hes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/5hes ftp://data.pdbj.org/pub/pdb/validation_reports/he/5hes | HTTPS FTP |
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-Related structure data
Related structure data | 3dtcS 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: 35232.301 Da / Num. of mol.: 2 / Fragment: UNP residues 5-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZAK, MLTK, HCCS4 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9NYL2, mitogen-activated protein kinase kinase kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM bis-tris-propane pH 6.5, 200 mM sodium malonate, 20% PEG3350, 10% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→78.7 Å / Num. obs: 44222 / % possible obs: 99.6 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.14→2.21 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.302 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3450 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DTC Resolution: 2.14→78.7 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.14→78.7 Å
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