[English] 日本語
![](img/lk-miru.gif)
- PDB-6gnp: Crystal Structure Of Sea Bream Transthyretin in complex with 3,5,... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6gnp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Of Sea Bream Transthyretin in complex with 3,5,6-trichloro-2-pyridinol (TC2P) | ||||||
![]() | Transthyretin | ||||||
![]() | TRANSPORT PROTEIN / transthyretin / thyroxine disrupting chemicals / TDCs / 3 / 5 / 6-trichloro-2-pyridinol / TC2P | ||||||
Function / homology | ![]() thyroid hormone binding / purine nucleobase metabolic process / hormone activity / extracellular space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grundstrom, C. / Zhang, J. / Olofsson, A. / Andersson, P.L. / Sauer-Eriksson, A.E. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 110.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 84.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6gnmC ![]() 6gnoC ![]() 6gnrC ![]() 6gnwC ![]() 6gonC ![]() 6gooC ![]() 6gr7C ![]() 6grpC ![]() 1sn2S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 14455.096 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.81 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. TC2P was added at 5 x molar excess to the protein. The reservoir contained 30% PEG 8K, 0.1M ...Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. TC2P was added at 5 x molar excess to the protein. The reservoir contained 30% PEG 8K, 0.1M NaCacodylate pH 6.5, 0.2M AmSO4. Drop size 3 plus 3 microliter |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.7 Å / Num. obs: 38625 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.053 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2704 / % possible all: 95.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1sn2 Resolution: 2.019→46.7 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.63
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.019→46.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|