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- PDB-2aky: HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2aky | ||||||
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Title | HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER | ||||||
![]() | ADENYLATE KINASE | ||||||
![]() | ADENYLATE KINASE / ATP:AMP PHOSPHOTRANSFERASE / MYOKINASE | ||||||
Function / homology | ![]() pre-replicative complex assembly / AMP metabolic process / ADP biosynthetic process / Interconversion of nucleotide di- and triphosphates / adenylate kinase / adenylate kinase activity / nucleotide metabolic process / DNA replication origin binding / DNA replication initiation / ATP metabolic process ...pre-replicative complex assembly / AMP metabolic process / ADP biosynthetic process / Interconversion of nucleotide di- and triphosphates / adenylate kinase / adenylate kinase activity / nucleotide metabolic process / DNA replication origin binding / DNA replication initiation / ATP metabolic process / mitochondrial intermembrane space / mitochondrion / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Abele, U. / Schulz, G.E. | ||||||
![]() | ![]() 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: ![]() Title: Stability, Activity and Structure of Adenylate Kinase Mutants Authors: Spuergin, P. / Abele, U. / Schulz, G.E. #2: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.6 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 699.2 KB | Display | ![]() |
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Full document | ![]() | 700.3 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 |
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Components
#1: Protein | Mass: 24068.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: RED STAR, MILWAUKEE / Cellular location: CYTOSOL / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-AP5 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % | |||||||||||||||||||||||||||||||||||
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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: 1.5418 Å |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: 1988 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.96 Å / Num. obs: 15638 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % |
Reflection | *PLUS Lowest resolution: 9999 Å |
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Processing
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Refinement | Resolution: 1.96→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→10 Å
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Refine LS restraints |
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