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Yorodumi- PDB-1aky: HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aky | ||||||
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Title | HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER | ||||||
Components | ADENYLATE KINASE | ||||||
Keywords | TRANSFERASE (PHOSPHOTRANSFERASE) / ATP:AMP PHOSPHOTRANSFERASE / MYOKINASE | ||||||
Function / homology | Function and homology information Interconversion of nucleotide di- and triphosphates / AMP metabolic process / ADP biosynthetic process / adenylate kinase / adenylate kinase activity / nucleotide metabolic process / DNA replication initiation / ATP metabolic process / mitochondrial intermembrane space / phosphorylation ...Interconversion of nucleotide di- and triphosphates / AMP metabolic process / ADP biosynthetic process / adenylate kinase / adenylate kinase activity / nucleotide metabolic process / DNA replication initiation / ATP metabolic process / mitochondrial intermembrane space / phosphorylation / mitochondrion / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.63 Å | ||||||
Authors | Abele, U. / Schulz, G.E. | ||||||
Citation | Journal: Protein Sci. / Year: 1995 Title: High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer. Authors: Abele, U. / Schulz, G.E. #1: Journal: Eur.J.Biochem. / Year: 1995 Title: Stability, Activity and Structure of Adenylate Kinase Mutants Authors: Spuergin, P. / Abele, U. / Schulz, G.E. #2: Journal: Nucleic Acids Res. / Year: 1987 Title: The C-DNA Sequence Encoding Cytosolic Adenylate Kinase from Baker'S Yeast (Saccharomyces Cerevisiae) Authors: Proba, K. / Tomasselli, A.G. / Nielsen, P. / Schulz, G.E. #3: Journal: J.Mol.Biol. / Year: 1987 Title: Structure of the Complex of Yeast Adenylate Kinase with the Inhibitor Ap5A at 2.6 Angstroms Resolution Authors: Egner, U. / Tomasselli, A.G. / Schulz, G.E. #4: Journal: Eur.J.Biochem. / Year: 1986 Title: The Complete Amino Acid Sequence of Adenylate Kinase from Baker'S Yeast Authors: Tomasselli, A.G. / Mast, E. / Janes, W. / Schiltz, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aky.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aky.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 1aky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/1aky ftp://data.pdbj.org/pub/pdb/validation_reports/ak/1aky | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 92 |
-Components
#1: Protein | Mass: 24068.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: FALA STRASBOURG / Cellular location: CYTOSOL / Production host: Escherichia coli (E. coli) / References: UniProt: P07170, adenylate kinase |
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#2: Chemical | ChemComp-AP5 / |
#3: Chemical | ChemComp-IMD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.08 % | |||||||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 46 % | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.54 |
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Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: 1990 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.63 Å / Num. obs: 27634 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.076 |
Reflection | *PLUS Lowest resolution: 9999 Å / Rmerge(I) obs: 0.076 |
-Processing
Software |
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Refinement | Resolution: 1.63→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |