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- PDB-6gr7: Crystal Structure Of Human Transthyretin in complex with 2,4,5-tr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gr7 | ||||||
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Title | Crystal Structure Of Human Transthyretin in complex with 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) | ||||||
![]() | Transthyretin | ||||||
![]() | TRANSPORT PROTEIN / transthyretin / thyroxine disrupting chemicals / TDCs / 2 / 4 / 5-trichlorophenoxyacetic acid / 5-T | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Grundstrom, C. / Zhang, J. / Olofsson, A. / Andersson, P.L. / Sauer-Eriksson, A.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Interspecies Variation between Fish and Human Transthyretins in Their Binding of Thyroid-Disrupting Chemicals. Authors: Zhang, J. / Grundstrom, C. / Brannstrom, K. / Iakovleva, I. / Lindberg, M. / Olofsson, A. / Andersson, P.L. / Sauer-Eriksson, A.E. #1: ![]() Title: Structure-Based Virtual Screening Protocol for in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin. Authors: Zhang, J. / Begum, A. / Brannstrom, K. / Grundstrom, C. / Iakovleva, I. / Olofsson, A. / Sauer-Eriksson, A.E. / Andersson, P.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.9 KB | Display | ![]() |
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PDB format | ![]() | 69.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6gnmC ![]() 6gnoC ![]() 6gnpC ![]() 6gnrC ![]() 6gnwC ![]() 6gonC ![]() 6gooC ![]() 6grpC ![]() 1f41S S: Starting model for refinement C: citing same article ( |
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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: 13777.360 Da / Num. of mol.: 2 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: 2.14 Å3/Da / Density % sol: 42.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: The purified human TTR was dialyzed against 10 mM Na-phosphate buffer with 100 mM KCl (pH 7.6) and concentrated to 5 mg/mL The reservoir contained 28% PEG 4K, 0.1M NaAc pH 4.5, 0.2M AmAc. ...Details: The purified human TTR was dialyzed against 10 mM Na-phosphate buffer with 100 mM KCl (pH 7.6) and concentrated to 5 mg/mL The reservoir contained 28% PEG 4K, 0.1M NaAc pH 4.5, 0.2M AmAc. Drop size 3 plus 3 microliter. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→42.7 Å / Num. obs: 46647 / % possible obs: 98.5 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4301 / % possible all: 89.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1F41 Resolution: 1.4→42.7 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→42.7 Å
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Refine LS restraints |
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LS refinement shell |
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