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Open data
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Basic information
Entry | Database: PDB / ID: 9avs | ||||||
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Title | Human alpha-galactosidase A in complex with saposin B | ||||||
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![]() | HYDROLASE / Galactosidase / GLA / Saposin / SapB / Fabry disease / Lysosomal / Activator protein | ||||||
Function / homology | ![]() positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / glycosylceramide catabolic process / ganglioside GM1 binding / negative regulation of nitric-oxide synthase activity / ganglioside GT1b binding / alpha-galactosidase ...positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / glycosylceramide catabolic process / ganglioside GM1 binding / negative regulation of nitric-oxide synthase activity / ganglioside GT1b binding / alpha-galactosidase / alpha-galactosidase activity / glycosphingolipid catabolic process / oligosaccharide metabolic process / glycoside catabolic process / galactoside binding / sphingolipid metabolic process / negative regulation of nitric oxide biosynthetic process / prostate gland growth / epithelial cell differentiation involved in prostate gland development / Glycosphingolipid catabolism / lysosomal transport / azurophil granule membrane / regulation of lipid metabolic process / catalytic activity / enzyme activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / lysosomal lumen / Peptide ligand-binding receptors / regulation of autophagy / phospholipid binding / azurophil granule lumen / late endosome / Platelet degranulation / G alpha (i) signalling events / scaffold protein binding / collagen-containing extracellular matrix / protease binding / lysosome / hydrolase activity / lysosomal membrane / intracellular membrane-bounded organelle / signaling receptor binding / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sawyer, T.K. / Garman, S.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Human Saposin B Ligand Binding and Presentation to alpha-Galactosidase A. Authors: Sawyer, T.K. / Aral, E. / Staros, J.V. / Bobst, C.E. / Garman, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.8 KB | Display | ![]() |
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PDB format | ![]() | 150.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 31.2 KB | Display | |
Data in CIF | ![]() | 42.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9axgC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 47344.465 Da / Num. of mol.: 2 / Mutation: D170A Source method: isolated from a genetically manipulated source Details: C-terminal double Flag-tag / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 9097.452 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Fragment corresponds to residues 195-273 of canonical isoform P07602-1. Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 5 types, 6 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
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#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / | |
-Non-polymers , 2 types, 16 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-SO4 / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 500 nL of protein (0.1 mM GLA plus 0.22 mM SapB) was mixed with 500 nL of reservoir solution (0.1 mM Tris pH 8.0, 1 M Ammonium sulfate) and equilibrated against 70 uL reservoirs at 20 C. |
-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: Nov 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3.53→57.23 Å / Num. obs: 20451 / % possible obs: 99 % / Redundancy: 12.9 % / Biso Wilson estimate: 90.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.237 / Net I/σ(I): 7.12 |
Reflection shell | Resolution: 3.53→3.656 Å / Rmerge(I) obs: 1.057 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2023 / CC1/2: 0.903 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.53→57.23 Å
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Refine LS restraints |
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LS refinement shell |
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