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- PDB-6gfh: Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gfh | ||||||
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Title | Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with neo-IP5 and ATP | ||||||
![]() | Inositol-pentakisphosphate 2-kinase | ||||||
![]() | TRANSFERASE / IPK1 / MYO-IP5 | ||||||
Function / homology | ![]() inositol-1,4,5,6-tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / inositol phosphate biosynthetic process / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / phosphorylation ...inositol-1,4,5,6-tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / inositol phosphate biosynthetic process / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / phosphorylation / defense response to virus / defense response to bacterium / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Whitfield, H.L. / Brearley, C.A. / Hemmings, A.M. | ||||||
![]() | ![]() Title: A Fluorescent Probe Identifies Active Site Ligands of Inositol Pentakisphosphate 2-Kinase. Authors: Whitfield, H. / Gilmartin, M. / Baker, K. / Riley, A.M. / Godage, H.Y. / Potter, B.V.L. / Hemmings, A.M. / Brearley, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.5 KB | Display | ![]() |
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PDB format | ![]() | 148.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6fjkC ![]() 6fl3C ![]() 6fl8C ![]() 6gfgC ![]() 2xamS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52863.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A178UAB5, UniProt: Q93YN9*PLUS, inositol-pentakisphosphate 2-kinase |
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-Non-polymers , 7 types, 125 molecules ![](data/chem/img/K7V.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-B3P / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.13 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18 % PEG 3350, 0.1 M bis-tris propane pH 6.5, 2 mM MgCl2, 25% EG or 35% PEG 3350, 0.1 M bis-tris propane pH 6.5, 2 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 31, 2012 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.65→29.34 Å / Num. obs: 27766 / % possible obs: 90.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 47.33 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.11 / Rrim(I) all: 0.169 / Net I/σ(I): 3.5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2XAM Resolution: 2.65→29.335 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108 Å2 / Biso mean: 52.4975 Å2 / Biso min: 19.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→29.335 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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