8V06 | pdb_00008v06

Crystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA for 9 days

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF13918	PLD-like domain (PLDc_3)	PLD-like domain		Domain
A, C	PF13918	PLD-like domain (PLDc_3)	PLD-like domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	5'-3' exonuclease PLD3	single-stranded DNA 5'-3' DNA exonuclease activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity single-stranded DNA 5'-3' DNA exonuclease activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity phosphoric ester hydrolase activity phospholipase activity phosphoric diester hydrolase activity glycerophospholipase activity D-type glycerophospholipase activity lipase activity cation binding ion binding binding metal ion binding small molecule binding	multicellular organismal process regulation of cellular process response to stimulus regulation of cytokine production involved in inflammatory response response to stress cytokine production regulation of cytokine production regulation of multicellular organismal process production of molecular mediator involved in inflammatory response regulation of biosynthetic process regulation of biological process defense response biological regulation regulation of macromolecule metabolic process multicellular organismal process regulation of cellular process response to stimulus regulation of cytokine production involved in inflammatory response response to stress cytokine production regulation of cytokine production regulation of multicellular organismal process production of molecular mediator involved in inflammatory response regulation of biosynthetic process regulation of biological process defense response biological regulation regulation of macromolecule metabolic process cytokine production involved in inflammatory response gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process inflammatory response macromolecule metabolic process regulation of metabolic process biological process involved in interspecies interaction between organisms immune response response to other organism defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus primary metabolic process lipid metabolic process developmental process muscle structure development cellular developmental process cell differentiation anatomical structure development striated muscle cell differentiation muscle cell differentiation myotube differentiation	cellular anatomical structure endomembrane system vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cellular anatomical structure endomembrane system vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome Golgi membrane Golgi apparatus endosome membrane early endosome endosome intracellular vesicle early endosome membrane cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane vesicle membrane-enclosed lumen vacuolar lumen lysosomal lumen intracellular organelle lumen organelle lumen late endosome membrane late endosome organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
A, C	5'-3' exonuclease PLD3	single-stranded DNA 5'-3' DNA exonuclease activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity single-stranded DNA 5'-3' DNA exonuclease activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity phosphoric ester hydrolase activity phospholipase activity phosphoric diester hydrolase activity glycerophospholipase activity D-type glycerophospholipase activity lipase activity cation binding ion binding binding metal ion binding small molecule binding	multicellular organismal process regulation of cellular process response to stimulus regulation of cytokine production involved in inflammatory response response to stress cytokine production regulation of cytokine production regulation of multicellular organismal process production of molecular mediator involved in inflammatory response regulation of biosynthetic process regulation of biological process defense response biological regulation regulation of macromolecule metabolic process multicellular organismal process regulation of cellular process response to stimulus regulation of cytokine production involved in inflammatory response response to stress cytokine production regulation of cytokine production regulation of multicellular organismal process production of molecular mediator involved in inflammatory response regulation of biosynthetic process regulation of biological process defense response biological regulation regulation of macromolecule metabolic process cytokine production involved in inflammatory response gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process inflammatory response macromolecule metabolic process regulation of metabolic process biological process involved in interspecies interaction between organisms immune response response to other organism defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus primary metabolic process lipid metabolic process developmental process muscle structure development cellular developmental process cell differentiation anatomical structure development striated muscle cell differentiation muscle cell differentiation myotube differentiation	cellular anatomical structure endomembrane system vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cellular anatomical structure endomembrane system vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome Golgi membrane Golgi apparatus endosome membrane early endosome endosome intracellular vesicle early endosome membrane cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane vesicle membrane-enclosed lumen vacuolar lumen lysosomal lumen intracellular organelle lumen organelle lumen late endosome membrane late endosome organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR050874	Diverse function phospholipase D-related protein	Family
B, D	IPR001736	Phospholipase D/Transphosphatidylase	Domain
B, D	IPR032803	PLD3/4-like, PLD-like domain	Domain
A, C	IPR050874	Diverse function phospholipase D-related protein	Family
A, C	IPR001736	Phospholipase D/Transphosphatidylase	Domain
A, C	IPR032803	PLD3/4-like, PLD-like domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C	NEP	Parent Component: HIS RESID: AA0035 PSI-MOD : 1'-phospho-L-histidine MOD:00044

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.