[English] 日本語
![](img/lk-miru.gif)
- PDB-3dx0: Golgi alpha-Mannosidase II in complex with Mannostatin A at pH 5.75 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3dx0 | ||||||
---|---|---|---|---|---|---|---|
Title | Golgi alpha-Mannosidase II in complex with Mannostatin A at pH 5.75 | ||||||
![]() | 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. / Rose, D.R. | ||||||
![]() | ![]() Title: The molecular basis of inhibition of Golgi alpha-mannosidase II by mannostatin A. Authors: Kuntz, D.A. / Zhong, W. / Guo, J. / Rose, D.R. / Boons, G.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 250.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 195.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 502 KB | Display | |
Data in XML | ![]() | 47.5 KB | Display | |
Data in CIF | ![]() | 75.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dx1C ![]() 3dx2C ![]() 3dx3C ![]() 3dx4C ![]() 1htyS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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 |
---|---|
#2: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 1167 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MSN.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MSN.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / |
---|---|
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-MSN / ( |
#6: Chemical | ChemComp-MPD / ( |
#7: Water | ChemComp-HOH / |
-Details
Sequence details | E970K CONFLICT IN UNP ENTRY Q24451 |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.04 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG8000, Tris, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Nov 23, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54182 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 116271 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.0544 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4090 / % possible all: 94.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1HTY Resolution: 1.7→19.57 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.966 / SU B: 1.454 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.092 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.97 Å2 / Biso mean: 13.239 Å2 / Biso min: 2.82 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.57 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|