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- PDB-2ak3: THE THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN MITOCHONDR... -
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Open data
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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 | |||||||||
![]() | ADENYLATE KINASE ISOENZYME-3 | |||||||||
![]() | TRANSFERASE (PHOSPHOTRANSFERASE) | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Diederichs, K. / Schulz, G.E. | |||||||||
![]() | ![]() 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: ![]() Title: The Three-Dimensional Structure of the Complex between Mitochondrial Matrix Adenylate Kinase and its Substrate AMP Authors: Diederichs, K. / Schulz, G.E. #2: ![]() Title: Induced-Fit Movements in Adenylate Kinase Authors: Schulz, G.E. / Muller, C.W. / Diederichs, K. #3: ![]() 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: ![]() Title: The Complete Primary Structure of GTP:AMP Phosphotransferase from Beef Heart Mitochondria Authors: Tomasselli, A.G. / Frank, R. / Schiltz, E. #5: ![]() 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: ![]() Title: Mitochondrial GTP-AMP Phosphotransferase: 1. Purification and Properties Authors: Tomasselli, A.G. / Schirmer, R.H. / Noda, L.H. #7: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.9 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501.7 KB | Display | ![]() |
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Full document | ![]() | 511.2 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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: (0.985, 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 | |
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Components
#1: Protein | Mass: 25575.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P08760, nucleoside-triphosphate-adenylate kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 |
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Processing
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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 |