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Yorodumi- PDB-7w9q: Crystal structure of V30M-TTR in complex with naringenin derivative-14 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w9q | ||||||
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Title | Crystal structure of V30M-TTR in complex with naringenin derivative-14 | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Amyloidosis / Complex / Inhibitor / thyroxine | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å | ||||||
Authors | Katayama, W. / Shimane, A. / Nabeshima, Y. / Yokoyama, T. / Mizuguchi, M. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Chlorinated Naringenin Analogues as Potential Inhibitors of Transthyretin Amyloidogenesis. Authors: Mizuguchi, M. / Nakagawa, Y. / Inui, K. / Katayama, W. / Sawai, Y. / Shimane, A. / Kitakami, R. / Okada, T. / Nabeshima, Y. / Yokoyama, T. / Kanamitsu, K. / Nakagawa, S. / Toyooka, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w9q.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w9q.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 7w9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w9q_validation.pdf.gz | 1006.3 KB | Display | wwPDB validaton report |
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Full document | 7w9q_full_validation.pdf.gz | 1009.7 KB | Display | |
Data in XML | 7w9q_validation.xml.gz | 13 KB | Display | |
Data in CIF | 7w9q_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/7w9q ftp://data.pdbj.org/pub/pdb/validation_reports/w9/7w9q | HTTPS FTP |
-Related structure data
Related structure data | 7w9rC 4n85S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17342.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.71 Å3/Da / Density % sol: 27.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, NaOAc, CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.599→35.51 Å / Num. obs: 31948 / % possible obs: 99.5 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rrim(I) all: 0.049 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3058 / CC1/2: 0.774 / Rrim(I) all: 0.792 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4n85 Resolution: 1.599→35.507 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.599→35.507 Å
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Refine LS restraints |
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LS refinement shell |
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