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- PDB-4btx: Crystal structure of human vascular adhesion protein-1 in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4btx | |||||||||
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Title | Crystal structure of human vascular adhesion protein-1 in complex with pyridazinone inhibitors | |||||||||
![]() | MEMBRANE PRIMARY AMINE OXIDASE | |||||||||
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Function / homology | ![]() aliphatic amine oxidase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bligt-Linden, E. / Pihlavisto, M. / Szatmari, I. / Otwinowski, Z. / Smith, D.J. / Lazar, L. / Fulop, F. / Salminen, T.A. | |||||||||
![]() | ![]() Title: Novel Pyridazinone Inhibitors for Vascular Adhesion Protein- 1 (Vap-1): Old Target - New Inhibition Mode. Authors: Bligt-Linden, E. / Pihlavisto, M. / Szatmari, I. / Otwinowski, Z. / Smith, D.J. / Lazar, L. / Fulop, F. / Salminen, T.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 | ![]() | 303.8 KB | Display | ![]() |
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PDB format | ![]() | 242.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4btwC ![]() 4btyC ![]() 1us1S C: citing same article ( S: Starting model for refinement |
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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: 81896.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Sugars , 4 types, 10 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/MAN.gif)
#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 | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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 | ||
#6: Sugar | ChemComp-NAG / ![]() #8: Sugar | ChemComp-MAN / | ![]() |
-Non-polymers , 4 types, 300 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/WF8.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/WF8.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ![]() #5: Chemical | ChemComp-CA / #7: Chemical | #9: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.91 Å3/Da / Density % sol: 74.75 % / Description: NONE |
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Crystal grow![]() | Details: 0.6-0.75 M NA/K TARTRATE, 0.2 M NACL, 0.1 M HEPES PH 7.4-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 5, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.78→50 Å / Num. obs: 62917 / % possible obs: 99.9 % / Observed criterion σ(I): 2.36 / Redundancy: 7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.78→2.83 Å / Redundancy: 5.4 % / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1US1 Resolution: 2.78→49.05 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.889 / SU B: 10.586 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.467 / ESU R Free: 0.31 / 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 mean: 39.991 Å2
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Refinement step | Cycle: LAST / Resolution: 2.78→49.05 Å
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Refine LS restraints |
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