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- PDB-4bty: 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: 4bty | |||||||||
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Title | Crystal structure of human vascular adhesion protein-1 in complex with pyridazinone inhibitors | |||||||||
![]() | MEMBRANE PRIMARY AMINE OXIDASE | |||||||||
![]() | OXIDOREDUCTASE | |||||||||
Function / homology | ![]() primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response ...primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response / copper ion binding / protein heterodimerization activity / response to antibiotic / calcium ion binding / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / membrane / plasma membrane / cytoplasm 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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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 300.2 KB | Display | ![]() |
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PDB format | ![]() | 239.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 57.6 KB | Display | |
Data in CIF | ![]() | 77.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4btwC ![]() 4btxC ![]() 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 Details: TYR471 POST TRANSLATIONALLY MODIFIED TO TOPAQUINONE Source: (natural) ![]() |
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-Sugars , 3 types, 9 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 48 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/JWF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/JWF.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-CA / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.03 Å3/Da / Density % sol: 75.37 % / 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: MARRESEARCH / Detector: CCD / Date: May 5, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 43449 / % possible obs: 98.7 % / Observed criterion σ(I): 1.17 / Redundancy: 4.3 % / Rmerge(I) obs: 0.29 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 3 % / % possible all: 92.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1US1 Resolution: 3.1→49.2 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.902 / SU B: 16.977 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / 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 |
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Refinement step | Cycle: LAST / Resolution: 3.1→49.2 Å
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Refine LS restraints |
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