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- PDB-1h86: COVALENT ADDUCT BETWEEN POLYAMINE OXIDASE AND N1ethylN11((cyclohe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h86 | |||||||||
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Title | COVALENT ADDUCT BETWEEN POLYAMINE OXIDASE AND N1ethylN11((cycloheptyl)methyl)4,8diazaundecane at pH 7.0 | |||||||||
![]() | POLYAMINE OXIDASE | |||||||||
![]() | OXIDOREDUCTASE / FLAVIN-DEPENDENT AMINE OXIDASE | |||||||||
Function / homology | ![]() polyamine oxidase (propane-1,3-diamine-forming) / N8-acetylspermidine oxidase (propane-1,3-diamine-forming) / spermine oxidase (propane-1,3-diamine-forming) activity / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / polyamine oxidase activity / polyamine catabolic process / spermine catabolic process / plant-type cell wall / apoplast / flavin adenine dinucleotide binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Binda, C. / Coda, A. / Angelini, R. / Federico, R. / Ascenzi, P. / Mattevi, A. | |||||||||
![]() | ![]() Title: Structural Bases for Inhibitor Binding and Catalysis in Polyamine Oxidase Authors: Binda, C. / Angelini, R. / Federico, R. / Ascenzi, P. / Mattevi, 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 | ![]() | 312.1 KB | Display | ![]() |
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PDB format | ![]() | 250.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 786.2 KB | Display | ![]() |
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Full document | ![]() | 817.9 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 52.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h81C ![]() 1h82C ![]() 1h83C ![]() 1h84C ![]() 1b37S 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 53698.457 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O64411, polyamine oxidase (propane-1,3-diamine-forming), N8-acetylspermidine oxidase (propane-1,3-diamine-forming) |
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-Sugars , 3 types, 4 molecules 
#2: 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 |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar |
-Non-polymers , 3 types, 797 molecules 




#4: Chemical | #5: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | CATALYSES THE OXIDATION OF THE SECONDARY AMINO GROUP OF POLYAMINES (SPERMINE, SPERMIDINE AND THEIR ...CATALYSES THE OXIDATION OF THE SECONDARY AMINO GROUP OF POLYAMINES |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.05 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 174933 / % possible obs: 94.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.094 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.198 / % possible all: 93.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Redundancy: 3.2 % / Num. measured all: 599120 |
Reflection shell | *PLUS % possible obs: 93.2 % / Mean I/σ(I) obs: 4.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1B37 Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5D / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection Rfree: 1745 / % reflection Rfree: 2 % / Rfactor Rfree: 0.229 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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