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Yorodumi- PDB-2roy: TRANSTHYRETIN (ALSO CALLED PREALBUMIN) COMPLEX WITH 3',5'-DINITRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2roy | |||||||||
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Title | TRANSTHYRETIN (ALSO CALLED PREALBUMIN) COMPLEX WITH 3',5'-DINITRO-N-ACETYL-L-THYRONINE | |||||||||
Components | TRANSTHYRETIN | |||||||||
Keywords | TRANSPORT / ALBUMIN / RETINOL-BINDING / VITAMIN A / AMYLOID / THYROID HORMONE / LIVER / PLASMA / CEREBROSPINAL FLUID / POLYNEUROPATHY / DISEASE MUTATION / THYROXINE / PREALBUMIN | |||||||||
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 / Resolution: 2.2 Å | |||||||||
Authors | Wojtczak, A. / Cody, V. / Luft, J.R. / Pangborn, W. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Structures of human transthyretin complexed with thyroxine at 2.0 A resolution and 3',5'-dinitro-N-acetyl-L-thyronine at 2.2 A resolution. Authors: Wojtczak, A. / Cody, V. / Luft, J.R. / Pangborn, W. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Structural Aspects of Inotropic Bipyridine Binding. Crystal Structure Determination to 1.9 A of the Human Serum Transthyretin-Milrinone Complex Authors: Wojtczak, A. / Luft, J.R. / Cody, V. #2: Journal: J.Biol.Chem. / Year: 1992 Title: Mechanism of Molecular Recognition. Structural Aspects of 3,3'-Diiodo-L-Thyronine Binding to Human Serum Transthyretin Authors: Wojtczak, A. / Luft, J. / Cody, V. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Crystal Structure Determination at 2.3-A Resolution of Human Transthyretin-3',5'-Dibromo-2',4,4',6-Tetrahydroxyaurone Complex Authors: Ciszak, E. / Cody, V. / Luft, J.R. #4: Journal: Nature / Year: 1977 Title: Protein-DNA and Protein-Hormone Interactions in Prealbumin: A Model of the Thyroid Hormone Nuclear Receptor? Authors: Blake, C.C. / Oatley, S.J. #7: Journal: J.Mol.Biol. / Year: 1974 Title: Structure of Human Plasma Prealbumin at 2.5 A Resolution. A Preliminary Report on the Polypeptide Chain Conformation, Quaternary Structure and Thyroxine Binding Authors: Blake, C.C.F. / Geisow, M.J. / Swan, I.D. / Rerat, C. / Rerat, B. #8: Journal: J.Mol.Biol. / Year: 1971 Title: An X-Ray Study of the Subunit Structure of Prealbumin Authors: Blake, C.C. / Swan, I.D. / Rerat, C. / Berthou, J. / Laurent, A. / Rerat, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2roy.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2roy.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 2roy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2roy_validation.pdf.gz | 483.1 KB | Display | wwPDB validaton report |
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Full document | 2roy_full_validation.pdf.gz | 507.1 KB | Display | |
Data in XML | 2roy_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 2roy_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/2roy ftp://data.pdbj.org/pub/pdb/validation_reports/ro/2roy | HTTPS FTP |
-Related structure data
-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: 13777.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PLASMA / Tissue: PLASMA / References: UniProt: P02766 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.36 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.9 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 12450 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Num. measured all: 70011 / Rmerge(I) obs: 0.069 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→8 Å Details: THE MODEL CONTAINS THE 3', 5'-DINITRO-N-ACETYL-THYRONINE MOLECULE IN BOTH BINDING SITES. THE OCCUPANCY OF 50% REFLECTS THE PRESENCE OF CRYSTALLOGRAPHIC TWO-FOLD AXIS CAUSING STATISTICAL ...Details: THE MODEL CONTAINS THE 3', 5'-DINITRO-N-ACETYL-THYRONINE MOLECULE IN BOTH BINDING SITES. THE OCCUPANCY OF 50% REFLECTS THE PRESENCE OF CRYSTALLOGRAPHIC TWO-FOLD AXIS CAUSING STATISTICAL DISORDER OF THE LIGAND, AND CORRESPONDS TO SATURATION OF THE BINDING SITES.
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.63 Å2 |