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- PDB-8v06: Crystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8v06 | |||||||||
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Title | Crystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA for 9 days | |||||||||
![]() | (5'-3' exonuclease ...) x 2 | |||||||||
![]() | HYDROLASE / PLD3 / phospholipase / phosphohistidine / nuclease | |||||||||
Function / homology | ![]() spleen exonuclease / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Role of phospholipids in phagocytosis / phospholipase D activity / regulation of cytokine production involved in inflammatory response / lysosomal lumen / late endosome membrane / early endosome membrane / inflammatory response ...spleen exonuclease / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Role of phospholipids in phagocytosis / phospholipase D activity / regulation of cytokine production involved in inflammatory response / lysosomal lumen / late endosome membrane / early endosome membrane / inflammatory response / lysosomal membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yuan, M. / Wilson, I.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4. Authors: Yuan, M. / Peng, L. / Huang, D. / Gavin, A. / Luan, F. / Tran, J. / Feng, Z. / Zhu, X. / Matteson, J. / Wilson, I.A. / Nemazee, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 661.3 KB | Display | ![]() |
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PDB format | ![]() | 544.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 61.5 KB | Display | |
Data in CIF | ![]() | 83.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8v05C ![]() 8v07C ![]() 8v08C 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
-5'-3' exonuclease ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 51935.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 51856.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 4 types, 8 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 #6: Sugar | |
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-Non-polymers , 2 types, 189 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: 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: 2.85 Å3/Da / Density % sol: 56.84 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 1.6 M ammonium sulfate, 0.5 mM magnesium chloride, 0.1 M citric acid, pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |