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Yorodumi- PDB-1ake: STRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ake | ||||||
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Title | STRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHIA COLI AND THE INHIBITOR AP5A REFINED AT 1.9 ANGSTROMS RESOLUTION: A MODEL FOR A CATALYTIC TRANSITION STATE | ||||||
Components | ADENYLATE KINASE | ||||||
Keywords | TRANSFERASE(PHOSPHOTRANSFERASE) | ||||||
Function / homology | Function and homology information purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Mueller, C.W. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1992 Title: Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state. Authors: Muller, C.W. / Schulz, G.E. #1: Journal: J.Mol.Biol. / Year: 1990 Title: Induced-Fit Movements in Adenylate Kinases Authors: Schulz, G.E. / Mueller, C.W. / Diederichs, K. #2: Journal: J.Mol.Biol. / Year: 1988 Title: Structure of the Complex of Adenylate Kinase from Escherichia Coli with the Inhibitor P1, P5-Bis (Adenosine-5'-) Pentaphosphate Authors: Mueller, C.W. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ake.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ake.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 1ake.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ake_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1ake_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1ake_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 1ake_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/1ake ftp://data.pdbj.org/pub/pdb/validation_reports/ak/1ake | 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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Atom site foot note | 1: CIS PROLINE - PRO A 87 / 2: CIS PROLINE - PRO B 87 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.995341, 0.068333, 0.068023), Vector: Details | THE TRANSFORMATION PRESENTED ON THE *MTRIX* RECORDS WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. | |
-Components
#1: Protein | Mass: 23620.029 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.17 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.7 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 202.909-912 1988 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 9999 Å / Num. obs: 40700 / % possible obs: 94.1 % / Num. measured all: 156159 / Rmerge(I) obs: 0.147 |
Reflection shell | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 1.98 Å / % possible obs: 92.8 % / Num. unique obs: 7170 / Rmerge(I) obs: 0.805 |
-Processing
Software |
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Refinement | Resolution: 2→10 Å / Rfactor Rwork: 0.196 / Rfactor obs: 0.196 / σ(F): 0 Details: IN COMPLEX-I ARG 167 AND PHOSPHATE-4 OF AP5 ADOPT TWO CONFORMATIONS. BOTH CONFORMATIONS WERE REFINED ALTERNATINGLY. NOTE THAT THE DISTANCE PD - O3D FOR CONFORMATION A OF AP5 A 215 IS 2.13 ...Details: IN COMPLEX-I ARG 167 AND PHOSPHATE-4 OF AP5 ADOPT TWO CONFORMATIONS. BOTH CONFORMATIONS WERE REFINED ALTERNATINGLY. NOTE THAT THE DISTANCE PD - O3D FOR CONFORMATION A OF AP5 A 215 IS 2.13 ANGSTROMS WHICH IS LARGER THAN EXPECTED. NOTE FURTHER THAT CONFORMATION A OF THIS ENTRY CORRESPONDS TO CONFORMATION A' OF THE PAPER CITED ON JRNL RECORDS ABOVE AND CONFORMATION B CORRESPONDS TO CONFORMATION B' OF THE PUBLICATION. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor all: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.2 |