+Open data
-Basic information
Entry | Database: PDB / ID: 7yaw | ||||||
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Title | Crystal structure of ZAK in complex with compound YH-180 | ||||||
Components | Mitogen-activated protein kinase kinase kinase MLT | ||||||
Keywords | STRUCTURAL PROTEIN/INHIBITOR / ZAK / Inhibitor / YH-180 / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-INHIBITOR 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 / stress-activated protein kinase signaling cascade / positive regulation of programmed cell death ...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 / stress-activated protein kinase signaling cascade / positive regulation of programmed cell death / regulation of mitotic metaphase/anaphase transition / limb development / embryonic digit morphogenesis / cellular response to UV-B / protein kinase activator activity / pyroptotic inflammatory response / p38MAPK cascade / MAP kinase kinase kinase activity / stress-activated MAPK cascade / JNK cascade / cytoskeleton organization / DNA damage checkpoint signaling / chromosome segregation / cellular response to gamma radiation / MAPK cascade / ribosome binding / small ribosomal subunit rRNA binding / protein autophosphorylation / cell differentiation / inflammatory response / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / RNA binding / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kong, L.L. / Yun, C.H. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: Rational Design of Covalent Kinase Inhibitors by an Integrated Computational Workflow (Kin-Cov). Authors: Zhou, Y. / Yu, H. / Vind, A.C. / Kong, L. / Liu, Y. / Song, X. / Tu, Z. / Yun, C. / Smaill, J.B. / Zhang, Q.W. / Ding, K. / Bekker-Jensen, S. / Lu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yaw.cif.gz | 246.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yaw.ent.gz | 202.5 KB | Display | PDB format |
PDBx/mmJSON format | 7yaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yaw_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7yaw_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7yaw_validation.xml.gz | 50 KB | Display | |
Data in CIF | 7yaw_validation.cif.gz | 68.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/7yaw ftp://data.pdbj.org/pub/pdb/validation_reports/ya/7yaw | HTTPS FTP |
-Related structure data
Related structure data | 7yazC 5x5oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35337.504 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZAK / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9NYL2, mitogen-activated protein kinase kinase kinase #2: Chemical | ChemComp-IGS / ~{ #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: 2.58 Å3/Da / Density % sol: 52.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.05 M Magnesium acetate, 0.05 M Sodium acetate pH 5.0, 28% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→31.69 Å / Num. obs: 83627 / % possible obs: 96 % / Redundancy: 20 % / Biso Wilson estimate: 28.13 Å2 / Rpim(I) all: 0.05 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.1→2.15 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 5784 / Rpim(I) all: 0.487 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X5O Resolution: 2.1→31.69 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.14 / 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: 105.04 Å2 / Biso mean: 35.2366 Å2 / Biso min: 12.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→31.69 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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