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Yorodumi- PDB-6q9o: HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 10 AT 1.21A; Stru... -
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-Basic information
Entry | Database: PDB / ID: 6q9o | ||||||
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Title | HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 10 AT 1.21A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes | ||||||
Components | E3 ubiquitin-protein ligase Mdm2 | ||||||
Keywords | LIGASE / PPI with p53 / inhibitor complex / cell cycle | ||||||
Function / homology | Function and homology information cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / receptor serine/threonine kinase binding ...cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / receptor serine/threonine kinase binding / Trafficking of AMPA receptors / positive regulation of vascular associated smooth muscle cell migration / peroxisome proliferator activated receptor binding / SUMO transferase activity / negative regulation of protein processing / response to steroid hormone / NEDD8 ligase activity / response to iron ion / AKT phosphorylates targets in the cytosol / cellular response to peptide hormone stimulus / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / cellular response to alkaloid / regulation of protein catabolic process / blood vessel development / cardiac septum morphogenesis / ligase activity / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to magnesium ion / SUMOylation of transcription factors / protein sumoylation / protein localization to nucleus / cellular response to UV-C / blood vessel remodeling / cellular response to estrogen stimulus / protein autoubiquitination / cellular response to actinomycin D / ribonucleoprotein complex binding / positive regulation of vascular associated smooth muscle cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / NPAS4 regulates expression of target genes / transcription repressor complex / regulation of heart rate / positive regulation of mitotic cell cycle / positive regulation of protein export from nucleus / proteolysis involved in protein catabolic process / response to cocaine / ubiquitin binding / Stabilization of p53 / Regulation of RUNX3 expression and activity / protein destabilization / RING-type E3 ubiquitin transferase / establishment of protein localization / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / response to toxic substance / cellular response to gamma radiation / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / disordered domain specific binding / endocytic vesicle membrane / ubiquitin protein ligase activity / Signaling by ALK fusions and activated point mutants / Regulation of TP53 Degradation / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of neuron projection development / cellular response to hypoxia / 5S rRNA binding / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / regulation of cell cycle / Ub-specific processing proteases / protein ubiquitination / response to xenobiotic stimulus / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / negative regulation of apoptotic process / apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / zinc ion binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.21 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 | 6q9o.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q9o.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 6q9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/6q9o ftp://data.pdbj.org/pub/pdb/validation_reports/q9/6q9o | HTTPS FTP |
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-Related structure data
Related structure data | 6q96C 6q9hC 6q9lC 6q9qC 6q9sC 6q9uC 6q9wC 6q9yC 4oq3S 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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Unit cell |
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-Components
#1: Protein | Mass: 11156.052 Da / Num. of mol.: 2 / Fragment: N-terminal domain, p53 binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2 / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q00987, RING-type E3 ubiquitin transferase #2: Chemical | #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: 1.91 Å3/Da / Density % sol: 35.72 % / Mosaicity: 0.241 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.4M AmSO4, 0.1M NaCitrate, 0.2M NaCl, 0.1M TRIS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2009 |
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→50 Å / Num. obs: 50939 / % possible obs: 99.5 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.069 / Χ2: 1.054 / Net I/σ(I): 28.44 |
Reflection shell | Resolution: 1.21→1.25 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 4.54 / Num. unique obs: 5176 / Χ2: 1.827 / % possible all: 95.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OQ3 Resolution: 1.21→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.966 / SU ML: 0.02 / SU R Cruickshank DPI: 0.0426 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.037 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: 43.32 Å2 / Biso mean: 12.183 Å2 / Biso min: 5.73 Å2
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Refinement step | Cycle: final / Resolution: 1.21→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.211→1.242 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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