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Yorodumi- PDB-1thc: CRYSTAL STRUCTURE DETERMINATION AT 2.3A OF HUMAN TRANSTHYRETIN-3'... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1thc | ||||||
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Title | CRYSTAL STRUCTURE DETERMINATION AT 2.3A OF HUMAN TRANSTHYRETIN-3',5'-DIBROMO-2',4,4',6-TETRA-HYDROXYAURONE COMPLEX | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | TRANSPORT (THYROXINE / RETINOL) IN SERUM | ||||||
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: 2.3 Å | ||||||
Authors | Ciszak, E. / Cody, V. / Luft, J.R. | ||||||
Citation | 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. #1: 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. #2: Journal: Nature / Year: 1977 Title: Protein-DNA and Protein-Hormone Interactions in Prealbumin, a Model of the Thyroid Hormone Nuclear Receptor (Query) Authors: Blake, C.C.F. / Oatley, S.J. #3: Journal: J.Mol.Biol. / Year: 1974 Title: Structure of Human Plasma Prealbumin at 2.5 Angstroms 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.A. / Rerat, C. / Rerat, B. #4: Journal: J.Mol.Biol. / Year: 1971 Title: An X-Ray Study of the Subunit Structure of Prealbumin Authors: Blake, C.C.F. / Swan, I.D.A. / Rerat, C. / Berthou, J. / Laurent, A. / Rerat, B. | ||||||
History |
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Remark 700 | SHEET THE FIRST STRAND OF THE *EXTERNAL* SHEET IN EACH SUBUNIT IS DISCONTINUOUS. TO ACCOMMODATE ...SHEET THE FIRST STRAND OF THE *EXTERNAL* SHEET IN EACH SUBUNIT IS DISCONTINUOUS. TO ACCOMMODATE THESE DISCONTINUITIES EACH *EXTERNAL* SHEET IS REPRESENTED HERE TWICE, WITH A DIFFERENT STRAND 1 IN EACH CASE. STRANDS 2,3,4 OF *X1A* ARE IDENTICAL TO STRANDS 2,3,4 OF *X2A*. SIMILARLY STRANDS 2,3,4 OF *X1B* ARE IDENTICAL TO STRANDS 2,3,4 OF *X2B*. THIS DESCRIPTION IS CONSISTENT WITH THAT USED BY BLAKE AND COWORKERS FOR THE NATIVE TRANSTHYRETIN (PROTEIN DATA BANK ENTRY 2PAB). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1thc.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1thc.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 1thc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1thc_validation.pdf.gz | 523.3 KB | Display | wwPDB validaton report |
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Full document | 1thc_full_validation.pdf.gz | 554.1 KB | Display | |
Data in XML | 1thc_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1thc_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/1thc ftp://data.pdbj.org/pub/pdb/validation_reports/th/1thc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13776.376 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02766 #2: Chemical | ChemComp-FL9 / #3: Water | ChemComp-HOH / | Nonpolymer details | THE STRUCTURE CONTAINS THE 3',5'-DIBROMO-2',4,4',6-TETRAHYDROXY AURONE MOLECULES THAT BIND IN TWO ...THE STRUCTURE CONTAINS THE 3',5'-DIBROMO-2',4,4',6-TETRAHYDRO | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.65 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6.9 / Method: batch method | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Num. obs: 11830 / Num. measured all: 18899 / Rmerge(I) obs: 0.05 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.179 / Highest resolution: 2.3 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.3 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 10 Å / Num. reflection obs: 8442 / σ(F): 2 / Rfactor all: 0.179 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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