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- PDB-2c11: Crystal structure of the 2-hydrazinopyridine of semicarbazide- se... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2c11 | ||||||||||||
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Title | Crystal structure of the 2-hydrazinopyridine of semicarbazide- sensitive amine oxidase | ||||||||||||
![]() | MEMBRANE COPPER AMINE OXIDASE | ||||||||||||
![]() | OXIDOREDUCTASE / ADHESION PROTEIN-1 / 2-HYDROXYPYRIDINE / METAL-BINDING / CELL ADHESION / GLYCOPROTEIN / SIGNAL-ANCHOR / TPQ / TRANSMEMBRANE | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Jakobsson, E. / Kleywegt, G.J. | ||||||||||||
![]() | ![]() Title: Structure of human semicarbazide-sensitive amine oxidase/vascular adhesion protein-1. Authors: Jakobsson, E. / Nilsson, J. / Ogg, D. / Kleywegt, G.J. | ||||||||||||
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 | ![]() | 541.8 KB | Display | ![]() |
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PDB format | ![]() | 445.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 112.8 KB | Display | |
Data in CIF | ![]() | 150.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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, 4 molecules ABCD
#1: Protein | Mass: 81775.734 Da / Num. of mol.: 4 / Fragment: EXTRA-CELLULAR DOMAINS, RESIDUES 29-763 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 6 types, 18 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 101 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-CA / #9: Chemical | ChemComp-CU / #10: Chemical | ChemComp-CL / #11: Water | ChemComp-HOH / | |
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-Details
Compound details | CELL ADHESION PROTEIN THAT IS INVOLVED IN THE BINDING OF LYMPHOCYTES TO PERIPHERAL LYMPH NODE ...CELL ADHESION PROTEIN THAT IS INVOLVED IN THE BINDING OF LYMPHOCYTE |
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Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.27 % Description: THE DATA IS TWINNED AND THE ESTIMATED TWINNING FRACTION IS 0.28. |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: THE PROTEIN WAS CRYSTALLISED IN 0.1 M KBR, 0.1 M ACETATE PH5, 38 % PEG1000 AT 288 K. THE CRYSTALS WERE SOAKED FOR FIVE DAYS IN 40 % PEG1000, 0.1 M ACETATE PH 5, 80 MM KBR, 5 MM CUCL2, 8 MM 2-HYDRAZINOPYRIDINE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→83.3 Å / Num. obs: 72802 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.9→3.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure: ![]() Details: THE LAST REFINEMENT ROUND WAS DONE AGAINST ALL DATA. THE DATA IS TWINNED AND HAS BEEN REFINED USING THE TWIN-REFINEMENT MODULE AND AN ESTIMATED TWINNING FRACTION OF 0.28.
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Displacement parameters | Biso mean: 60 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.03 Å / Total num. of bins used: 8 |