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- PDB-6zfa: Structure of the catalytic domain of human endo-alpha-mannosidase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zfa | |||||||||||||||
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Title | Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcIFG, alpha-1,2-mannobiose and hexatungstotellurate(VI) TEW | |||||||||||||||
![]() | Glycoprotein endo-alpha-1,2-mannosidase![]() | |||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. ...Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure of human endo-alpha-1,2-mannosidase (MANEA), an antiviral host-glycosylation target. Authors: Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zdcC ![]() 6zdfC ![]() 6zdkSC ![]() 6zdlC ![]() 6zfnC ![]() 6zfqC ![]() 6zj1C ![]() 6zj5C ![]() 6zj6C S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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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, 1 molecules AAA
#1: Protein | ![]() Mass: 44783.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q5SRI9, ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/GLC.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose |
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#7: Sugar | ChemComp-GLC / ![]() |
-Non-polymers , 5 types, 142 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TEW.gif)
![](data/chem/img/IFM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TEW.gif)
![](data/chem/img/IFM.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EPE / ![]() | ||||
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#4: Chemical | ChemComp-MG / | ||||
#5: Chemical | #6: Chemical | ChemComp-IFM / | ![]() #8: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.8 % / Description: hexagonal |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 200 mM MgCl2, 30% v/v PEG 400 (Alfa Aesar), 1 mM Anderson-Evans polyoxotungstate TEW. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→110.76 Å / Num. obs: 42149 / % possible obs: 100 % / Redundancy: 16.5 % / Biso Wilson estimate: 21.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.038 / Rrim(I) all: 0.153 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 16.6 % / Rmerge(I) obs: 0.939 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2447 / CC1/2: 0.782 / Rpim(I) all: 0.237 / Rrim(I) all: 0.969 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6ZDK Resolution: 1.8→110.757 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.113 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.343 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→110.757 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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