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Yorodumi- PDB-6q9s: HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 14 AT 2.4A: Structura... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q9s | ||||||
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Title | HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 14 AT 2.4A: Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes | ||||||
Components | Protein Mdm4 | ||||||
Keywords | APOPTOSIS / HDMX / MDM4 | ||||||
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 / regulation of cell cycle / protein ubiquitination / Ub-specific processing proteases / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Kallen, J. | ||||||
Citation | Journal: Chemmedchem / Year: 2019 Title: Structural States of Hdm2 and HdmX: X-ray Elucidation of Adaptations and Binding Interactions for Different Chemical Compound Classes. Authors: Kallen, J. / Izaac, A. / Chau, S. / Wirth, E. / Schoepfer, J. / Mah, R. / Schlapbach, A. / Stutz, S. / Vaupel, A. / Guagnano, V. / Masuya, K. / Stachyra, T.M. / Salem, B. / Chene, P. / ...Authors: Kallen, J. / Izaac, A. / Chau, S. / Wirth, E. / Schoepfer, J. / Mah, R. / Schlapbach, A. / Stutz, S. / Vaupel, A. / Guagnano, V. / Masuya, K. / Stachyra, T.M. / Salem, B. / Chene, P. / Gessier, F. / Holzer, P. / Furet, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q9s.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q9s.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 6q9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/6q9s ftp://data.pdbj.org/pub/pdb/validation_reports/q9/6q9s | HTTPS FTP |
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-Related structure data
Related structure data | 6q96C 6q9hC 6q9lC 6q9oC 6q9qSC 6q9uC 6q9wC 6q9yC 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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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ACB
#1: Protein | Mass: 11186.985 Da / Num. of mol.: 3 / Fragment: N-terminal domain, p53 binding domain / Mutation: C17S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MDM4, MDMX / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O15151 |
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-Non-polymers , 5 types, 59 molecules
#2: Chemical | #3: Chemical | ChemComp-O4B / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: 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: 3.7 Å3/Da / Density % sol: 66.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.25M AmSO4, 6% w/v 18-crown-ether, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2010 |
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.95 Å / Num. obs: 20849 / % possible obs: 99.6 % / Redundancy: 12.7 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.066 / Rrim(I) all: 0.064 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 4.8 / Rpim(I) all: 0.445 / Rrim(I) all: 0.611 / % possible all: 98.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q9Q Resolution: 2.4→19.95 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.825 / SU ML: 0.159 / SU R Cruickshank DPI: 0.3131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.235 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 159.12 Å2 / Biso mean: 51.795 Å2 / Biso min: 32.88 Å2
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Refinement step | Cycle: final / Resolution: 2.4→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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