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- PDB-3ejt: Golgi alpha-Mannosidase II in complex with 5-substituted swainson... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ejt | ||||||
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Title | Golgi alpha-Mannosidase II in complex with 5-substituted swainsonine analog:(5R)-5-[2'-(4-tert-butylphenyl)ethyl]-swainsonine | ||||||
![]() | Alpha-mannosidase 2 | ||||||
![]() | HYDROLASE / GH38 Glycosidase / Glycosidase / Golgi apparatus / Membrane / Metal-binding / Signal-anchor / Transmembrane | ||||||
Function / homology | ![]() mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / mannose metabolic process / N-glycan processing / Golgi stack ...mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / mannose metabolic process / N-glycan processing / Golgi stack / protein deglycosylation / protein glycosylation / carbohydrate binding / lysosome / Golgi membrane / endoplasmic reticulum / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kuntz, D.A. / Shea, K. / Rose, D.R. | ||||||
![]() | ![]() Title: Structural Investigation of the Binding of 5-Substituted Swainsonine Analogues to Golgi alpha-Mannosidase II. Authors: Kuntz, D.A. / Nakayama, S. / Shea, K. / Hori, H. / Uto, Y. / Nagasawa, H. / Rose, D.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 471.9 KB | Display | ![]() |
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PDB format | ![]() | 382.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796 KB | Display | ![]() |
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Full document | ![]() | 804.8 KB | Display | |
Data in XML | ![]() | 49.2 KB | Display | |
Data in CIF | ![]() | 78 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ejpC ![]() 3ejqC ![]() 3ejrC ![]() 3ejsC ![]() 3ejuC ![]() 3bubS 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 119701.617 Da / Num. of mol.: 1 / Fragment: Catalytic domain; UNP residues 76-1108 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase |
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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 1288 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HN6.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HN6.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-MRD / ( |
#5: Chemical | ChemComp-DMS / |
#6: Chemical | ChemComp-HN6 / ( |
#7: Water | ChemComp-HOH / |
-Details
Sequence details | E970K CONFLICT IN UNP ENTRY Q24451 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG8000, Tris, pH 7, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 21, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. all: 235192 / Num. obs: 233665 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.96 % / Rmerge(I) obs: 0.0824 / Net I/σ(I): 14.71 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 4.38 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 5.18 / Num. unique all: 5176 / % possible all: 97.3 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3BUB Resolution: 1.35→29.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.163 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.918 / SU B: 1.352 / SU ML: 0.026 / SU R Cruickshank DPI: 0.056 / SU Rfree: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 max: 84.27 Å2 / Biso mean: 14.852 Å2 / Biso min: 3.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→29.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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