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- PDB-3t7a: Crystal structure of the catalytic domain of human diphosphoinosi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3t7a | ||||||
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Title | Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP at pH 5.2 | ||||||
![]() | Inositol Pyrophosphate Kinase | ||||||
![]() | TRANSFERASE / ATP-grasp Fold / Inositol Pyrophosphate Kinase | ||||||
Function / homology | ![]() diphosphoinositol-pentakisphosphate 1-kinase / diphosphoinositol pentakisphosphate kinase activity / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / inositol hexakisphosphate kinase activity / Synthesis of pyrophosphates in the cytosol / inositol phosphate metabolic process ...diphosphoinositol-pentakisphosphate 1-kinase / diphosphoinositol pentakisphosphate kinase activity / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / inositol hexakisphosphate kinase activity / Synthesis of pyrophosphates in the cytosol / inositol phosphate metabolic process / inositol phosphate biosynthetic process / inositol metabolic process / sensory perception of sound / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, H. / Falck, J. / Hall, T.M.T. / Shears, S.B. | ||||||
![]() | ![]() Title: Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Authors: Wang, H. / Falck, J.R. / Hall, T.M. / Shears, S.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.9 KB | Display | ![]() |
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PDB format | ![]() | 68.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3t54SC ![]() 3t99C ![]() 3t9aC ![]() 3t9bC ![]() 3t9cC ![]() 3t9dC ![]() 3t9eC ![]() 3t9fC 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37568.891 Da / Num. of mol.: 1 / Fragment: ATP-grasp Kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O43314, diphosphoinositol-pentakisphosphate 1-kinase |
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-Non-polymers , 5 types, 443 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ADP / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, 1 mM ATP, 2 mM CdCl2 Soaking under pH5.2 overnight , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2011 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 45377 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rsym value: 0.057 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.423 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3T54 Resolution: 1.7→41.28 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.688 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.327 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→41.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.746 Å / Total num. of bins used: 20
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