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- PDB-3hii: Crystal structure of human diamine oxidase in complex with the in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hii | |||||||||
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Title | Crystal structure of human diamine oxidase in complex with the inhibitor pentamidine | |||||||||
![]() | Amiloride-sensitive amine oxidase | |||||||||
![]() | OXIDOREDUCTASE / copper amine oxidase / topaquinone / TPQ / diamine oxidase / DAO / human / pentamidine / Glycoprotein / Heparin-binding / Metal-binding / Secreted | |||||||||
Function / homology | ![]() diamine oxidase / putrescine metabolic process / histamine oxidase activity / : / : / putrescine oxidase activity / diamine oxidase activity / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds ...diamine oxidase / putrescine metabolic process / histamine oxidase activity / : / : / putrescine oxidase activity / diamine oxidase activity / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / bicellular tight junction / quinone binding / specific granule lumen / peroxisome / heparin binding / copper ion binding / response to antibiotic / calcium ion binding / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | McGrath, A.P. / Guss, J.M. | |||||||||
![]() | ![]() Title: Structure and inhibition of human diamine oxidase Authors: McGrath, A.P. / Hilmer, K.M. / Collyer, C.A. / Shepard, E.M. / Elmore, B.O. / Brown, D.E. / Dooley, D.M. / Guss, J.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 | ![]() | 326.9 KB | Display | ![]() |
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PDB format | ![]() | 258.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 59.6 KB | Display | |
Data in CIF | ![]() | 87.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hi7SC ![]() 3higC 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, 2 molecules AB
#1: Protein | Mass: 83463.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 6 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 |
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#3: Polysaccharide | 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 , 5 types, 925 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PNT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PNT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-GOL / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.24 % / Mosaicity: 0.431 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M bis-tris propane, 20%(w/v) PEG 3350, 0.2M sodium sulfate, pH 7.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 2008 / Details: OSMIC MIRRORS |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.149→50 Å / Num. all: 89751 / Num. obs: 89751 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 29.96 Å2 / Rmerge(I) obs: 0.103 / Χ2: 1.067 / Net I/σ(I): 9.903 |
Reflection shell | Resolution: 2.149→2.23 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.7 / Num. unique all: 8090 / Χ2: 1.041 / % possible all: 87.1 |
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Processing
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Refinement | Method to determine structure: BY REFINEMENT Starting model: PDB ENTRY 3HI7 Resolution: 2.149→25.84 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.866 / SU B: 4.494 / SU ML: 0.118 / SU R Cruickshank DPI: 0.245 / SU Rfree: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.23 Å2 / Biso mean: 21.017 Å2 / Biso min: 11.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.149→25.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.149→2.204 Å / Total num. of bins used: 20
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