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Yorodumi- PDB-2pab: STRUCTURE OF PREALBUMIN, SECONDARY, TERTIARY AND QUATERNARY INTER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pab | ||||||||||||
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Title | STRUCTURE OF PREALBUMIN, SECONDARY, TERTIARY AND QUATERNARY INTERACTIONS DETERMINED BY FOURIER REFINEMENT AT 1.8 ANGSTROMS | ||||||||||||
Components | TRANSTHYRETIN PRECURSOR | ||||||||||||
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: 1.8 Å | ||||||||||||
Authors | Oatley, S.J. / Blake, C.C.F. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 1978 Title: Structure of prealbumin: secondary, tertiary and quaternary interactions determined by Fourier refinement at 1.8 A. Authors: Blake, C.C. / Geisow, M.J. / Oatley, S.J. / Rerat, B. / Rerat, C. #1: 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. #2: 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. #3: 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 ACCOMODATE ...SHEET THE FIRST STRAND OF THE *EXTERNAL* SHEET IN EACH SUBUNIT IS DISCONTINUOUS. TO ACCOMODATE 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*. DESPITE THIS PARTIAL REDUNDANCY OF REPRESENTATION THERE IS NO IMPLICATION THAT EACH SUBUNIT CONTAINS MORE THAN ONE *EXTERNAL* SHEET SUBSTRUCTURE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pab.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pab.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 2pab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pab_validation.pdf.gz | 377.8 KB | Display | wwPDB validaton report |
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Full document | 2pab_full_validation.pdf.gz | 398.1 KB | Display | |
Data in XML | 2pab_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 2pab_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/2pab ftp://data.pdbj.org/pub/pdb/validation_reports/pa/2pab | 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (-0.98771, 0.156297),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. | |
-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) / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.84 % |
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Crystal grow | *PLUS Method: other / Details: Blake, C.C.F., (1974) J. Mol. Biol., 88, 1. |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å |
-Processing
Refinement | Resolution: 1.8→8 Å / Rfactor Rwork: 0.29 / Rfactor obs: 0.29 Details: THE AXES OF THE COORDINATE SYSTEM USED HERE ARE ALIGNED WITH THE CRYSTALLOGRAPHIC AXES BUT THE ORIGIN IS DISPLACED BY A/2, B/2, C/4 AS GIVEN IN THE SCALE RECORDS BELOW. | ||||||||||||
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refinement | *PLUS Rfactor obs: 0.289 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |