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- PDB-6rrw: GOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rrw | ||||||||||||
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Title | GOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3,4-Dihydro-2H-1,5-benzodioxepin-7-yl)benzyl]oxy}pentyl)-2-(hydroxymethyl)-3,4,5-piperidinetriol | ||||||||||||
![]() | Alpha-mannosidase 2 | ||||||||||||
![]() | HYDROLASE / Mannosidase / Glycoside Hydrolase | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Armstrong, Z. / Lahav, D. / Johnson, R. / Kuo, C.L. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M. / Geurink, P.P. ...Armstrong, Z. / Lahav, D. / Johnson, R. / Kuo, C.L. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M. / Geurink, P.P. / Ovaa, H. / van der Stelt, M. / Codee, J.D.C. / Aerts, J.M.F.G. / Wu, L. / Overkleeft, H.S. / Davies, G.J. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors. Authors: Armstrong, Z. / Kuo, C.L. / Lahav, D. / Liu, B. / Johnson, R. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M.F. / Florea, B.I. / Hissink, C. / Boot, R.G. / ...Authors: Armstrong, Z. / Kuo, C.L. / Lahav, D. / Liu, B. / Johnson, R. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M.F. / Florea, B.I. / Hissink, C. / Boot, R.G. / Geurink, P.P. / Ovaa, H. / van der Stelt, M. / van der Marel, G.M. / Codee, J.D.C. / Aerts, J.M.F.G. / Wu, L. / Overkleeft, H.S. / 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 | ![]() | 226.7 KB | Display | ![]() |
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PDB format | ![]() | 172.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 713.9 KB | Display | ![]() |
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Full document | ![]() | 719.8 KB | Display | |
Data in XML | ![]() | 37.4 KB | Display | |
Data in CIF | ![]() | 54.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rpcC ![]() 6rqzC ![]() 6rrhC ![]() 6rrjC ![]() 6rrnC ![]() 6rruC ![]() 6rrxC ![]() 6rryC ![]() 6rs0C ![]() 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 118208.000 Da / Num. of mol.: 1 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: Chemical | ChemComp-KG5 / ( |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M sodium succinate, pH 7.4 10 % PEG 3350 with microseeding |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→75.47 Å / Num. obs: 57896 / % possible obs: 97.6 % / Redundancy: 7 % / CC1/2: 0.998 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4531 / CC1/2: 0.787 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3bub Resolution: 2.15→75.47 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.229 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.39 Å2 / Biso mean: 41.175 Å2 / Biso min: 19.29 Å2
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Refinement step | Cycle: final / Resolution: 2.15→75.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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