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- PDB-6xy7: Human SHIP1 with magnesium and phosphate bound to the active site -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xy7 | ||||||
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Title | Human SHIP1 with magnesium and phosphate bound to the active site | ||||||
![]() | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 | ||||||
![]() | HYDROLASE / Phosphatidylinositol / phosphate / phosphatase / Alzheimer's Disease | ||||||
Function / homology | ![]() inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ...inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / negative regulation of monocyte differentiation / phosphatidylinositol dephosphorylation / negative regulation of immune response / phosphatidylinositol biosynthetic process / phosphate-containing compound metabolic process / negative regulation of bone resorption / positive regulation of B cell differentiation / Synthesis of IP3 and IP4 in the cytosol / negative regulation of B cell proliferation / negative regulation of osteoclast differentiation / PECAM1 interactions / Synthesis of PIPs at the plasma membrane / negative regulation of interleukin-6 production / regulation of immune response / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / negative regulation of signal transduction / positive regulation of erythrocyte differentiation / determination of adult lifespan / SH3 domain binding / Signaling by CSF1 (M-CSF) in myeloid cells / Downstream TCR signaling / T cell receptor signaling pathway / cytoskeleton / intracellular signal transduction / positive regulation of apoptotic process / membrane raft / apoptotic process / signal transduction / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bradshaw, W.J. / Scacioc, A. / Fernandez-Cid, A. / Mckinley, G. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2. Authors: Bradshaw, W.J. / Kennedy, E.C. / Moreira, T. / Smith, L.A. / Chalk, R. / Katis, V.L. / Benesch, J.L.P. / Brennan, P.E. / Murphy, E.J. / Gileadi, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 37.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5rw2C ![]() 5rw3C ![]() 5rw4C ![]() 5rw5C ![]() 5rw6C ![]() 5rw7C ![]() 5rw8C ![]() 5rw9C ![]() 5rwaC ![]() 5rwbC ![]() 5rwcC ![]() 5rwdC ![]() 5rweC ![]() 5rwfC ![]() 5rwgC ![]() 5rwhC ![]() 5rwiC ![]() 5rwjC ![]() 5rwkC ![]() 5rwlC ![]() 5rwmC ![]() 5rwnC ![]() 5rwoC ![]() 5rwpC ![]() 5rwqC ![]() 5rwrC ![]() 5rwsC ![]() 5rwtC ![]() 5rwuC ![]() 5rwvC ![]() 5rwwC ![]() 5rwxC ![]() 5rwyC ![]() 5rwzC ![]() 5rx0C ![]() 5rx1C ![]() 5rx2C ![]() 5rx3C ![]() 5rx4C ![]() 5rx5C ![]() 5rx6C ![]() 5rx7C ![]() 5rx8C ![]() 5rx9C ![]() 5rxaC ![]() 5rxbC ![]() 5rxcC ![]() 5rxdC ![]() 5rxeC ![]() 5rxfC ![]() 5rxgC ![]() 5rxhC ![]() 5rxiC ![]() 5rxjC ![]() 5rxkC ![]() 5rxlC ![]() 5rxmC ![]() 5rxoC ![]() 5rxpC ![]() 5rxqC ![]() 5rxrC ![]() 5rxsC ![]() 5rxtC ![]() 5rxuC ![]() 5rxvC ![]() 5rxwC ![]() 5rxxC ![]() 5rxyC ![]() 5rxzC ![]() 5ry0C ![]() 5ry1C ![]() 5ry2C ![]() 5ry3C ![]() 5ry4C ![]() 5ry5C ![]() 5ry6C ![]() 5ry7C ![]() 5ry8C ![]() 5ry9C ![]() 5ryaC ![]() 5rybC ![]() 5rycC ![]() 5rydC ![]() 5ryeC ![]() 5ryfC ![]() 5rygC ![]() 5ryhC ![]() 5ryiC ![]() 5ryjC ![]() 5rykC ![]() 5rylC ![]() 6ibdC ![]() 8pdgC ![]() 8pdhC ![]() 8pdiC ![]() 8pdjC ![]() 5okmS 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 AAA
#1: Protein | Mass: 52877.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q92835, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase, inositol-polyphosphate 5-phosphatase, phosphoinositide 5-phosphatase |
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-Non-polymers , 5 types, 495 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / | ||||
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#3: Chemical | ChemComp-PO4 / | ||||
#4: Chemical | #5: Chemical | ChemComp-PGE / | #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: 2.09 Å3/Da / Density % sol: 41.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM MES/imidazole, pH 6.5, 20 % PEG 500 MME, 10% PEG 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 1.086→59.193 Å / Num. obs: 159826 / % possible obs: 87.6 % / Redundancy: 26.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.03 / Rrim(I) all: 0.155 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.093→1.14 Å / Redundancy: 20.7 % / Rmerge(I) obs: 2.19 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7907 / CC1/2: 0.601 / Rpim(I) all: 0.48 / Rrim(I) all: 2.246 / % possible all: 59.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OKM Resolution: 1.086→59.193 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.277 / SU ML: 0.026 / Cross valid method: FREE R-VALUE / ESU R: 0.031 / ESU R Free: 0.031 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.339 Å2
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Refinement step | Cycle: LAST / Resolution: 1.086→59.193 Å
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Refine LS restraints |
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LS refinement shell |
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