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- PDB-6zjd: Crystal structure of human adenylate kinase 3, AK3, in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zjd | ||||||
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Title | Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor ATP | ||||||
![]() | GTP:AMP phosphotransferase AK3, mitochondrial | ||||||
![]() | TRANSFERASE / GTP:AMP PHOSPHOTRANSFERASE / Gp5A | ||||||
Function / homology | ![]() UTP metabolic process / ITP metabolic process / nucleoside-triphosphate-adenylate kinase / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / GTP metabolic process / blood coagulation / Factors involved in megakaryocyte development and platelet production ...UTP metabolic process / ITP metabolic process / nucleoside-triphosphate-adenylate kinase / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / GTP metabolic process / blood coagulation / Factors involved in megakaryocyte development and platelet production / mitochondrial matrix / phosphorylation / GTP binding / mitochondrion / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Grundstrom, C. / Rogne, P. / Wolf-Watz, M. / Sauer-Eriksson, A.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3. Authors: Rogne, P. / Dulko-Smith, B. / Goodman, J. / Rosselin, M. / Grundstrom, C. / Hedberg, C. / Nam, K. / Sauer-Eriksson, A.E. / Wolf-Watz, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74 KB | Display | ![]() |
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PDB format | ![]() | 52.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zjbC ![]() 6zjeC ![]() 1zd8S S: Starting model for refinement C: citing same article ( |
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Similar 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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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25599.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UIJ7, nucleoside-triphosphate-adenylate kinase |
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-Non-polymers , 5 types, 428 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ATP / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Purified hAK3 was dialyzed against 30 mM MOPS buffer with 50 mM NaCl pH 7.0 and concentrated to 15-20 mg per ml. The resevoir contained 0.2 M MgCl2, 0.1 M Tris pH 8.0 and 20% PEG 6000. Drop ...Details: Purified hAK3 was dialyzed against 30 mM MOPS buffer with 50 mM NaCl pH 7.0 and concentrated to 15-20 mg per ml. The resevoir contained 0.2 M MgCl2, 0.1 M Tris pH 8.0 and 20% PEG 6000. Drop size 1 plus 1 microliter. Cryo protection 30% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Mar 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→26.856 Å / Num. obs: 45601 / % possible obs: 96.2 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.023 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2335 / CC1/2: 0.887 / Rpim(I) all: 0.203 / % possible all: 79.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1zd8 Resolution: 1.75→26.856 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.26 Å2 / Biso mean: 19.8649 Å2 / Biso min: 5.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→26.856 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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