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Yorodumi- PDB-1tlm: STRUCTURAL ASPECTS OF INOTROPIC BIPYRIDINE BINDING: CRYSTAL STRUC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tlm | ||||||
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Title | STRUCTURAL ASPECTS OF INOTROPIC BIPYRIDINE BINDING: CRYSTAL STRUCTURE DETERMINATION TO 1.9 ANGSTROMS OF THE HUMAN SERUM TRANSTHYRETIN-MILRINONE COMPLEX | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | TRANSPORT(THYROXINE) | ||||||
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: 1.9 Å | ||||||
Authors | Wojtczak, A. / Luft, J. / Cody, V. | ||||||
Citation | 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. #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: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Crystal Structure Determination at 2.3 Angstroms Resolution of Human Transthyretin-3', 5'-Dibromo-2',4,4',6-Tetrahydroxyaurone Complex Authors: Ciszak, E. / Cody, V. / Luft, J.R. #3: 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. #6: 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. #7: 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 | 1tlm.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tlm.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tlm_validation.pdf.gz | 396.1 KB | Display | wwPDB validaton report |
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Full document | 1tlm_full_validation.pdf.gz | 413.6 KB | Display | |
Data in XML | 1tlm_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1tlm_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/1tlm ftp://data.pdbj.org/pub/pdb/validation_reports/tl/1tlm | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 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 | #3: Water | ChemComp-HOH / | Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.32 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 293 K / pH: 6.9 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.89 Å / Num. obs: 16482 / % possible obs: 79 % / Num. measured all: 46029 / Rmerge(I) obs: 0.06 |
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Reflection shell | *PLUS Highest resolution: 1.89 Å / Lowest resolution: 2.01 Å / % possible obs: 36 % |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.9→8 Å Details: THIS COORDINATE SET COMPRISES TWO CHAINS REPRESENTING TWO CHEMICALLY EQUIVALENT, BUT CRYSTALLOGRAPHICALLY DISTINCT, ENTITIES. THE OTHER HALF OF THE COMPLETE TETRAMER MAY BE GENERATED FROM ...Details: THIS COORDINATE SET COMPRISES TWO CHAINS REPRESENTING TWO CHEMICALLY EQUIVALENT, BUT CRYSTALLOGRAPHICALLY DISTINCT, ENTITIES. THE OTHER HALF OF THE COMPLETE TETRAMER MAY BE GENERATED FROM THIS DIMER BY THE APPLICATION OF THE CRYSTALLOGRAPHIC DIAD PARALLEL TO Z THROUGH THE ORIGIN OF THIS COORDINATE SYSTEM, I. E. XPRIME=-X, YPRIME=-Y, ZPRIME=Z.
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 16162 / σ(F): 2 / Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |