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Yorodumi- PDB-4btx: Crystal structure of human vascular adhesion protein-1 in complex... -
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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 | |||||||||
Components | MEMBRANE PRIMARY AMINE OXIDASE | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information 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 / protein heterodimerization activity / copper ion binding / response to antibiotic / calcium ion binding / cell surface / Golgi apparatus / endoplasmic reticulum / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å | |||||||||
Authors | Bligt-Linden, E. / Pihlavisto, M. / Szatmari, I. / Otwinowski, Z. / Smith, D.J. / Lazar, L. / Fulop, F. / Salminen, T.A. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4btx.cif.gz | 303.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4btx.ent.gz | 242.9 KB | Display | PDB format |
PDBx/mmJSON format | 4btx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/4btx ftp://data.pdbj.org/pub/pdb/validation_reports/bt/4btx | HTTPS FTP |
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-Related structure data
Related structure data | 4btwC 4btyC 1us1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) HOMO SAPIENS (human) / Tissue: SERUM / References: UniProt: Q16853, primary-amine oxidase |
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-Sugars , 4 types, 10 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 | 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
#4: Chemical | #5: Chemical | ChemComp-CA / #7: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
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: 0.8726 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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