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Yorodumi- PDB-5vk1: Crystal structure of human MDM4 in complex with a 12-mer lysine-c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vk1 | ||||||
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Title | Crystal structure of human MDM4 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI | ||||||
Components |
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Keywords | SIGNALING PROTEIN/INHIBITOR / MDMX / MDMX-PEPTIDE INHIBITOR COMPLEX / ONCOPROTEIN / METAL-BINDING / NUCLEUS / ZINC-FINGER / stapled peptide / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process / Regulation of TP53 Activity through Methylation / ubiquitin-protein transferase activity / Regulation of TP53 Degradation / cellular response to hypoxia / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / protein stabilization / protein ubiquitination / regulation of cell cycle / Ub-specific processing proteases / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Tolbert, W.D. / Gohain, N. / Pazgier, M. | ||||||
Citation | Journal: Chem Sci / Year: 2019 Title: Dithiocarbamate-inspired side chain stapling chemistry for peptide drug design. Authors: Li, X. / Tolbert, W.D. / Hu, H.G. / Gohain, N. / Zou, Y. / Niu, F. / He, W.X. / Yuan, W. / Su, J.C. / Pazgier, M. / Lu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vk1.cif.gz | 284.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vk1.ent.gz | 235.4 KB | Display | PDB format |
PDBx/mmJSON format | 5vk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/5vk1 ftp://data.pdbj.org/pub/pdb/validation_reports/vk/5vk1 | HTTPS FTP |
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-Related structure data
Related structure data | 5vk0C 3eqyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 9575.293 Da / Num. of mol.: 8 / Fragment: residues 24-108 / Mutation: Q68A, Q69A, E70A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15151 #2: Protein/peptide | Mass: 1543.828 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 2.01 Å3/Da / Density % sol: 38.8 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% 2-propanol, 30% PEG 3350, and 100 mM Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→50 Å / Num. obs: 16330 / % possible obs: 86 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.69→2.75 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1.1 / Num. unique all: 704 / % possible all: 78.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3eqy Resolution: 2.69→50 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.815 / SU B: 60.775 / SU ML: 0.64 / Cross valid method: THROUGHOUT / ESU R Free: 0.605 / 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: 54.37 Å2
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Refinement step | Cycle: 1 / Resolution: 2.69→50 Å
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