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Yorodumi- PDB-4lwu: The 1.14A Crystal Structure of Humanized Xenopus MDM2 with RO5499252 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lwu | ||||||
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Title | The 1.14A Crystal Structure of Humanized Xenopus MDM2 with RO5499252 | ||||||
Components | E3 ubiquitin-protein ligase Mdm2 | ||||||
Keywords | Ligase/Ligase inhibitor / MDM2 / Spiroindolinone / E3 Ubiquitin Ligase / p53 / Nucleus / Ligase-Ligase inhibitor complex | ||||||
Function / homology | Function and homology information regulation of biological quality / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / regulation of cell cycle / apoptotic process / nucleolus / negative regulation of apoptotic process / nucleoplasm / identical protein binding / metal ion binding ...regulation of biological quality / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / regulation of cell cycle / apoptotic process / nucleolus / negative regulation of apoptotic process / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Graves, B.J. / Lukacs, C. / Janson, C.A. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2014 Title: Discovery of potent and selective spiroindolinone MDM2 inhibitor, RO8994, for cancer therapy. Authors: Zhang, Z. / Ding, Q. / Liu, J.J. / Zhang, J. / Jiang, N. / Chu, X.J. / Bartkovitz, D. / Luk, K.C. / Janson, C. / Tovar, C. / Filipovic, Z.M. / Higgins, B. / Glenn, K. / Packman, K. / Vassilev, L.T. / Graves, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lwu.cif.gz | 34.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lwu.ent.gz | 22.7 KB | Display | PDB format |
PDBx/mmJSON format | 4lwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/4lwu ftp://data.pdbj.org/pub/pdb/validation_reports/lw/4lwu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9831.419 Da / Num. of mol.: 1 / Fragment: N-terminal Domain (UNP Residues 21-105) / Mutation: I50L, P92H, L95I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: mdm2 / Plasmid: PUBS 520 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P56273, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Chemical | ChemComp-20U / ( |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.37 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 40-50% Saturated Ammonium Sulfate, 0.1M MES, pH 6.5, 5% PEG200, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→40.55 Å / Num. all: 29503 / Num. obs: 29503 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.14→1.2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.6 / Num. unique all: 4037 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→39.17 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 889077.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.5613 Å2 / ksol: 0.365742 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.14→39.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.14→1.2 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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