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- PDB-2b14: The crystal structure of 2,4-dinitrophenol in complex with the am... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2b14 | ||||||
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Title | The crystal structure of 2,4-dinitrophenol in complex with the amyloidogenic variant Transthyretin Leu 55 Pro | ||||||
![]() | Transthyretin | ||||||
![]() | TRANSPORT PROTEIN / AMYLOID / TRANSTHYRETIN / 2 / 4-DINITROPHENOL / Tetramer Stabilizer | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morais-de-Sa, E. / Neto-Silva, R.M. / Pereira, P.J. / Saraiva, M.J. / Damas, A.M. | ||||||
![]() | ![]() Title: The binding of 2,4-dinitrophenol to wild-type and amyloidogenic transthyretin Authors: Morais-de-Sa, E. / Neto-Silva, R.M. / Pereira, P.J. / Saraiva, M.J. / Damas, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.5 KB | Display | ![]() |
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PDB format | ![]() | 40.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.3 KB | Display | ![]() |
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Full document | ![]() | 450.8 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b15C ![]() 2b16C ![]() 1f86S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 13761.317 Da / Num. of mol.: 2 / Mutation: L55P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.38 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG550, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→50.85 Å / Num. all: 16093 / Num. obs: 16093 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.073 / Rsym value: 0.066 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2→2.09 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1909 / Rsym value: 0.162 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1F86 Resolution: 2→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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