[English] 日本語
![](img/lk-miru.gif)
- PDB-5kij: Crystal structure of the class I human endoplasmic reticulum 1,2-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5kij | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase and Man9GlcNAc2-PA complex | |||||||||||||||
![]() | Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase | |||||||||||||||
![]() | HYDROLASE / alpha/alpha-barrel / cation replacement / protein-glycan interaction | |||||||||||||||
Function / homology | ![]() mannoprotein catabolic process / Defective MAN1B1 causes MRT15 / protein alpha-1,2-demannosylation / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum quality control compartment / oligosaccharide metabolic process / protein glycosylation / ERAD pathway / ER Quality Control Compartment (ERQC) ...mannoprotein catabolic process / Defective MAN1B1 causes MRT15 / protein alpha-1,2-demannosylation / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum quality control compartment / oligosaccharide metabolic process / protein glycosylation / ERAD pathway / ER Quality Control Compartment (ERQC) / trans-Golgi network / extracellular vesicle / cytoplasmic vesicle / Maturation of spike protein / viral protein processing / endosome / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Karaveg, K. / Xiang, Y. / Moremen, K.W. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Substrate recognition and catalysis by GH47 alpha-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway. Authors: Xiang, Y. / Karaveg, K. / Moremen, K.W. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 130.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 96 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 880.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 884 KB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 39.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kk7C ![]() 5kkbC ![]() 1x9dS 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
#1: Protein | Mass: 52030.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9UKM7, mannosyl-oligosaccharide 1,2-alpha-mannosidase |
---|---|
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 613 molecules ![](data/chem/img/LA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BU1.gif)
![](data/chem/img/1PS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BU1.gif)
![](data/chem/img/1PS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-LA / | ||||||
---|---|---|---|---|---|---|---|
#4: Chemical | #5: Chemical | ChemComp-BU1 / #6: Chemical | ChemComp-1PS / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.72 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 24% PEG 4000, 50mM ammonium sulfate, 0.1M MES, 10% 1,4-butanediol, pH 6.5, 200mM NDSB-200, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.649→48.69 Å / Num. obs: 53113 / % possible obs: 96.5 % / Redundancy: 1.9 % / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.649→1.691 Å |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1X9D Resolution: 1.649→27.081 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 2.03 / Phase error: 23.04 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.649→27.081 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|