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- PDB-7ov2: Crystal structure of pig purple acid phosphatase in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ov2 | |||||||||
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Title | Crystal structure of pig purple acid phosphatase in complex with L-glutamine, (poly)ethylene glycol fragments and glycerol | |||||||||
![]() | Tartrate-resistant acid phosphatase type 5 | |||||||||
![]() | ![]() ![]() | |||||||||
Function / homology | ![]() Vitamin B2 (riboflavin) metabolism / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Feder, D. / McGeary, R.P. / Guddat, L.W. / Schenk, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach. Authors: Feder, D. / Mohd-Pahmi, S.H. / Hussein, W.M. / Guddat, L.W. / McGeary, R.P. / Schenk, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.4 KB | Display | ![]() |
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PDB format | ![]() | 78.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ov3C ![]() 7ov8C ![]() 1uteS ![]() 6vkb 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 / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 35154.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
-Non-polymers , 12 types, 276 molecules ![](data/chem/img/1PE.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/GLN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/GLN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ChemComp-P6G / | ![]() #5: Chemical | ![]() #6: Chemical | ChemComp-GLN / ![]() #7: Chemical | ChemComp-PO4 / | ![]() #8: Chemical | ChemComp-EDO / ![]() #9: Chemical | ChemComp-PGE / ![]() #10: Chemical | ChemComp-GOL / ![]() #11: Chemical | ChemComp-CIT / | ![]() #12: Chemical | ChemComp-NA / | #13: Chemical | ![]() #14: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.51 % / Description: Rod-shaped purple crystals |
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Crystal grow![]() | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 25% (W/V) PEG3350, 0.1 M LICL, 5% (V/V)ISOPROPANOL, 0.1 M SODIUM CITRATE PH 5.0, PROTEIN CONCENTRATION 38 MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→77.01 Å / Num. obs: 20575 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 19.98 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.052 / Rrim(I) all: 0.141 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.1→2.21 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2938 / CC1/2: 0.905 / Rpim(I) all: 0.193 / Rrim(I) all: 0.528 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1UTE Resolution: 2.1→51.25 Å / SU ML: 0.1711 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.7341
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→51.25 Å
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Refine LS restraints |
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LS refinement shell |
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