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Yorodumi- PDB-2ak3: THE THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN MITOCHONDR... -
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-Basic information
Entry | Database: PDB / ID: 2ak3 | |||||||||
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Title | THE THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN MITOCHONDRIAL MATRIX ADENYLATE KINASE AND ITS SUBSTRATE AMP AT 1.85 ANGSTROMS RESOLUTION | |||||||||
Components | ADENYLATE KINASE ISOENZYME-3 | |||||||||
Keywords | TRANSFERASE (PHOSPHOTRANSFERASE) | |||||||||
Function / homology | Function and homology information ITP metabolic process / nucleoside-triphosphate-adenylate kinase / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / Factors involved in megakaryocyte development and platelet production / adenylate kinase activity / GTP metabolic process / mitochondrial matrix ...ITP metabolic process / nucleoside-triphosphate-adenylate kinase / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / Factors involved in megakaryocyte development and platelet production / adenylate kinase activity / GTP metabolic process / mitochondrial matrix / GTP binding / mitochondrion / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.85 Å | |||||||||
Authors | Diederichs, K. / Schulz, G.E. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1991 Title: The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 A resolution. Authors: Diederichs, K. / Schulz, G.E. #1: Journal: Biochemistry / Year: 1990 Title: The Three-Dimensional Structure of the Complex between Mitochondrial Matrix Adenylate Kinase and its Substrate AMP Authors: Diederichs, K. / Schulz, G.E. #2: Journal: J.Mol.Biol. / Year: 1990 Title: Induced-Fit Movements in Adenylate Kinase Authors: Schulz, G.E. / Muller, C.W. / Diederichs, K. #3: Journal: J.Biol.Chem. / Year: 1989 Title: Cloning and Characterization of Cdna for Mitochondrial GTP:AMP Phosphotransferase of Bovine Liver Authors: Yamada, M. / Shahjahan, M. / Tanabe, T. / Kishi, F. / Nakazawa, A. #4: Journal: FEBS Lett. / Year: 1986 Title: The Complete Primary Structure of GTP:AMP Phosphotransferase from Beef Heart Mitochondria Authors: Tomasselli, A.G. / Frank, R. / Schiltz, E. #5: Journal: Eur.J.Biochem. / Year: 1984 Title: The Amino Acid Sequence of GTP:AMP Phosphotransferase from Beef-Heart Mitochondria: Extensive Homology with Cytosolic Adenylate Kinase Authors: Wieland, B. / Tomasselli, A.G. / Noda, L.H. / Frank, R. / Schulz, G.E. #6: Journal: Eur.J.Biochem. / Year: 1979 Title: Mitochondrial GTP-AMP Phosphotransferase: 1. Purification and Properties Authors: Tomasselli, A.G. / Schirmer, R.H. / Noda, L.H. #7: Journal: Eur.J.Biochem. / Year: 1979 Title: Mitochondrial GTP-AMP Phosphotransferase: 2. Kinetic and Equilibrium Dialysis Studies Authors: Tomasselli, A.G. / Noda, L.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ak3.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ak3.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ak3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ak3_validation.pdf.gz | 501.7 KB | Display | wwPDB validaton report |
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Full document | 2ak3_full_validation.pdf.gz | 511.2 KB | Display | |
Data in XML | 2ak3_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 2ak3_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/2ak3 ftp://data.pdbj.org/pub/pdb/validation_reports/ak/2ak3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.985, 0.031, 0.171), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD M1 A 0 - A 219 B 0 - B 219 1.508 | |
-Components
#1: Protein | Mass: 25575.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) References: UniProt: P08760, nucleoside-triphosphate-adenylate kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | Highest resolution: 1.85 Å / Num. obs: 42879 / % possible obs: 94.5 % |
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Reflection | *PLUS Lowest resolution: 9999 Å / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Resolution: 1.85→10 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |