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Yorodumi- PDB-3an3: Human PPAR gamma ligand binding domain in complex with a gamma se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3an3 | ||||||
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Title | Human PPAR gamma ligand binding domain in complex with a gamma selective agonist MO3S | ||||||
Components | Peroxisome proliferator-activated receptor gamma | ||||||
Keywords | TRANSCRIPTION / mainly alpha / nuclear receptor | ||||||
Function / homology | Function and homology information Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane ...Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane / aerobic respiration / mitochondrial inner membrane / mitochondrion / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Oyama, T. / Ohashi, M. / Waku, T. / Miyachi, H. / Morikawa, K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Design, Synthesis, and Structural Analysis of Phenylpropanoic Acid-Type PPAR gamma-Selective Agonists: Discovery of Reversed Stereochemistry-Activity Relationship Authors: Ohashi, M. / Oyama, T. / Nakagome, I. / Satoh, M. / Nishio, Y. / Nobusada, H. / Hirono, S. / Morikawa, K. / Hashimoto, Y. / Miyachi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3an3.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3an3.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 3an3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3an3_validation.pdf.gz | 797.9 KB | Display | wwPDB validaton report |
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Full document | 3an3_full_validation.pdf.gz | 817.3 KB | Display | |
Data in XML | 3an3_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 3an3_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/3an3 ftp://data.pdbj.org/pub/pdb/validation_reports/an/3an3 | HTTPS FTP |
-Related structure data
Related structure data | 3an4C 2znoS C: citing same article (ref.) S: Starting model for refinement |
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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: 32530.652 Da / Num. of mol.: 2 / Fragment: Ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231 #2: Chemical | ChemComp-M7S / ( | #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: 2.53 Å3/Da / Density % sol: 51.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.8M SODIUM CITRATE, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 11, 2009 |
Radiation | Monochromator: FIXED EXIT SI 111 DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 28907 / Num. obs: 28907 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.6 / Num. unique all: 2841 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZNO Resolution: 2.3→29.52 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 255044.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.4815 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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