3RDE | pdb_00003rde

Crystal structure of the catalytic domain of porcine leukocyte 12-lipoxygenase

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	Lipoxygenase catalytic domain-like	8098525	4001373	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Lipoxygenase	8098526	3001410	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Lipoxygenase	8098526	3001410	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lipoxygenase	8098526	3001410	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lipoxygenase	8098526	3001410	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	CoV_NSP4_C	e3rdeD2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: CoV_NSP4_C	ECOD (v294.1)
C	CoV_NSP4_C	e3rdeC2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: CoV_NSP4_C	ECOD (v294.1)
B	CoV_NSP4_C	e3rdeB2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: CoV_NSP4_C	ECOD (v294.1)
A	APH	e3rdeA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: APH	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.245.10	Mainly Alpha	Up-down Bundle	Lipoxygenase-1	domain 5	CATH (4.3.0)
D	3.10.450.60	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
C	1.20.245.10	Mainly Alpha	Up-down Bundle	Lipoxygenase-1	domain 5	CATH (4.3.0)
C	3.10.450.60	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
B	1.20.245.10	Mainly Alpha	Up-down Bundle	Lipoxygenase-1	domain 5	CATH (4.3.0)
B	3.10.450.60	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
A	1.20.245.10	Mainly Alpha	Up-down Bundle	Lipoxygenase-1	domain 5	CATH (4.3.0)
A	3.10.450.60	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00305	Lipoxygenase (Lipoxygenase)	Lipoxygenase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Arachidonate 12-lipoxygenase, 12S-type	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen oxidoreductase activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen catalytic activity arachidonate 15-lipoxygenase activity dioxygenase activity ion binding binding phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen oxidoreductase activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen catalytic activity arachidonate 15-lipoxygenase activity dioxygenase activity ion binding binding phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding small molecule binding linoleate 13S-lipoxygenase activity arachidonate 12(S)-lipoxygenase activity cation binding transition metal ion binding iron ion binding metal ion binding	response to peptide response to stimulus response to chemical cellular response to interleukin-13 response to interleukin-13 response to cytokine cellular response to cytokine stimulus icosanoid metabolic process fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process small molecule metabolic process response to peptide response to stimulus response to chemical cellular response to interleukin-13 response to interleukin-13 response to cytokine cellular response to cytokine stimulus icosanoid metabolic process fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process small molecule metabolic process metabolic process cellular process lipoxygenase pathway monocarboxylic acid metabolic process lipid metabolic process developmental process multicellular organismal process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of MAPK cascade biological regulation positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion immune response regulation of adaptive immune response negative regulation of response to stimulus negative regulation of immune response negative regulation of biological process negative regulation of adaptive immune response adaptive immune response negative regulation of immune system process immune system process regulation of immune response regulation of immune system process glycerophospholipid biosynthetic process phosphatidylethanolamine metabolic process glycerophospholipid metabolic process lipid biosynthetic process phospholipid biosynthetic process phospholipid metabolic process phosphatidylethanolamine biosynthetic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process glycerolipid metabolic process phosphorus metabolic process intracellular receptor signaling pathway peroxisome proliferator activated receptor signaling pathway regulation of peroxisome proliferator activated receptor signaling pathway nuclear receptor-mediated signaling pathway unsaturated fatty acid metabolic process long-chain fatty acid biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process lipoxin biosynthetic process long-chain fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process fatty acid derivative biosynthetic process fatty acid biosynthetic process fatty acid derivative metabolic process unsaturated fatty acid biosynthetic process lipoxin A4 biosynthetic process lipoxin A4 metabolic process import into cell regulation of localization regulation of cellular component organization transport vesicle-mediated transport cellular component organization engulfment of apoptotic cell localization regulation of phagocytosis, engulfment membrane invagination phagocytosis cellular component organization or biogenesis apoptotic cell clearance plasma membrane invagination regulation of endocytosis membrane organization regulation of engulfment of apoptotic cell regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization phagocytosis, engulfment regulation of membrane invagination endocytosis cellular response to metal ion cellular response to chemical stimulus response to metal ion cellular response to calcium ion response to calcium ion regulation of defense response regulation of response to external stimulus defense response regulation of inflammatory response response to external stimulus response to stress regulation of response to stress inflammatory response positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process positive regulation of cellular component organization regulation of cellular component size cellular component biogenesis regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly positive regulation of protein polymerization protein-containing complex assembly actin filament-based process regulation of actin filament polymerization regulation of biological quality protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin cytoskeleton organization actin filament polymerization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of actin polymerization or depolymerization actin filament organization regulation of cellular component biogenesis positive regulation of supramolecular fiber organization regulation of organelle organization organelle organization regulation of protein polymerization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization positive regulation of actin filament polymerization cytoskeleton organization regulation of anatomical structure size arachidonate metabolic process olefinic compound metabolic process wound healing response to wounding lipid modification fatty acid oxidation lipid oxidation linoleic acid metabolic process cellular response to stress response to endoplasmic reticulum stress	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane lipid droplet intracellular organelle organelle membraneless organelle intracellular membraneless organelle cytoplasmic side of plasma membrane cytoplasmic side of membrane cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane lipid droplet intracellular organelle organelle membraneless organelle intracellular membraneless organelle cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR020834	Lipoxygenase, conserved site	Conserved Site
A, B, C, D	IPR001024	PLAT/LH2 domain	Domain
A, B, C, D	IPR001885	Lipoxygenase, mammalian	Family
A, B, C, D	IPR042062	Lipoxygenase, vertebrates, PLAT domain	Domain
A, B, C, D	IPR036392	PLAT/LH2 domain superfamily	Homologous Superfamily
A, B, C, D	IPR036226	Lipoxigenase, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR000907	Lipoxygenase	Family
A, B, C, D	IPR020833	Lipoxygenase, iron binding site	Binding Site
A, B, C, D	IPR013819	Lipoxygenase, C-terminal	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Monotopic/peripheral	All alpha monotopic/peripheral	Lipoxygenase	Lipoxygenases

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.