4ORY | pdb_00004ory

Three-dimensional structure of the C65A-K59A double mutant of Human lipocalin-type Prostaglandin D Synthase holo, second crystal form

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d4oryc_	All beta proteins	Lipocalins	Lipocalins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4oryd_	All beta proteins	Lipocalins	Lipocalins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4orye_	All beta proteins	Lipocalins	Lipocalins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d4oryf_	All beta proteins	Lipocalins	Lipocalins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d4oryh_	All beta proteins	Lipocalins	Lipocalins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d4oryg_	All beta proteins	Lipocalins	Lipocalins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4oryb_	All beta proteins	Lipocalins	Lipocalins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4orya_	All beta proteins	Lipocalins	Lipocalins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Lipocalins	8070914	3001332	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Lipocalins	8070914	3001332	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Lipocalins	8070914	3001332	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Lipocalins	8070914	3001332	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Lipocalins	8070914	3001332	SCOP2B (2022-06-29)
G	SCOP2 Family	Retinol binding protein-like	8070913	4002493	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Lipocalins	8070914	3001332	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Lipocalins	8070914	3001332	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lipocalins	8070914	3001332	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)
C		e4oryC1	A: avirulence protein AvrPiz-t homologs	X: avirulence protein AvrPiz-t homologs	H: avirulence protein AvrPiz-t homologs	T:	F:	ECOD (20:10:01)
D		e4oryD1	A: avirulence protein AvrPiz-t homologs	X: avirulence protein AvrPiz-t homologs	H: avirulence protein AvrPiz-t homologs	T:	F:	ECOD (20:10:01)
E		e4oryE1	A: avirulence protein AvrPiz-t homologs	X: avirulence protein AvrPiz-t homologs	H: avirulence protein AvrPiz-t homologs	T:	F:	ECOD (20:10:01)
F		e4oryF1	A: avirulence protein AvrPiz-t homologs	X: avirulence protein AvrPiz-t homologs	H: avirulence protein AvrPiz-t homologs	T:	F:	ECOD (20:10:01)
H		e4oryH1	A: avirulence protein AvrPiz-t homologs	X: avirulence protein AvrPiz-t homologs	H: avirulence protein AvrPiz-t homologs	T:	F:	ECOD (20:10:01)
G		e4oryG1	A: avirulence protein AvrPiz-t homologs	X: avirulence protein AvrPiz-t homologs	H: avirulence protein AvrPiz-t homologs	T:	F:	ECOD (20:10:01)
B		e4oryB1	A: avirulence protein AvrPiz-t homologs	X: avirulence protein AvrPiz-t homologs	H: avirulence protein AvrPiz-t homologs	T:	F:	ECOD (20:10:01)
A		e4oryA1	A: avirulence protein AvrPiz-t homologs	X: avirulence protein AvrPiz-t homologs	H: avirulence protein AvrPiz-t homologs	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
D	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
E	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
F	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
H	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
G	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
B	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
A	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00061	Lipocalin / cytosolic fatty-acid binding protein family (Lipocalin)	Lipocalin / cytosolic fatty-acid binding protein family	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid ...	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Prostaglandin-H2 D-isomerase	fatty acid binding organic acid binding binding ion binding anion binding lipid binding carboxylic acid binding monocarboxylic acid binding small molecule binding isoprenoid binding retinoid binding isomerase activity intramolecular oxidoreductase activity prostaglandin-D synthase activity fatty acid binding organic acid binding binding ion binding anion binding lipid binding carboxylic acid binding monocarboxylic acid binding small molecule binding isoprenoid binding retinoid binding isomerase activity intramolecular oxidoreductase activity prostaglandin-D synthase activity catalytic activity	biosynthetic process metabolic process cellular process macromolecule metabolic process gene expression macromolecule biosynthetic process establishment of organelle localization multicellular organismal process regulated exocytosis cellular localization response to stimulus transport cell activation involved in immune response leukocyte degranulation biosynthetic process metabolic process cellular process macromolecule metabolic process gene expression macromolecule biosynthetic process establishment of organelle localization multicellular organismal process regulated exocytosis cellular localization response to stimulus transport cell activation involved in immune response leukocyte degranulation myeloid leukocyte activation myeloid leukocyte mediated immunity vesicle-mediated transport leukocyte activation localization secretion by cell organelle localization leukocyte activation involved in immune response establishment of localization in cell mast cell activation leukocyte mediated immunity mast cell mediated immunity immune response secretion cell activation vacuolar localization export from cell mast cell degranulation establishment of localization myeloid cell activation involved in immune response immune effector process mast cell activation involved in immune response exocytosis immune system process lysosome localization rhythmic process circadian sleep/wake cycle, sleep circadian sleep/wake cycle regulation of biological process rhythmic behavior regulation of circadian sleep/wake cycle circadian rhythm biological regulation regulation of circadian rhythm regulation of behavior behavior circadian behavior regulation of multicellular organismal process sleep regulation of circadian sleep/wake cycle, sleep circadian sleep/wake cycle process icosanoid metabolic process prostaglandin metabolic process unsaturated fatty acid metabolic process oxoacid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process prostanoid metabolic process icosanoid biosynthetic process small molecule metabolic process prostaglandin biosynthetic process prostanoid biosynthetic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process fatty acid biosynthetic process unsaturated fatty acid biosynthetic process monocarboxylic acid metabolic process lipid metabolic process negative regulation of male germ cell proliferation regulation of cellular process sexual reproduction regulation of reproductive process reproductive process regulation of male germ cell proliferation negative regulation of biological process gamete generation germ cell proliferation regulation of germ cell proliferation negative regulation of cellular process negative regulation of cell population proliferation cell population proliferation multicellular organismal reproductive process male germ cell proliferation negative regulation of reproductive process regulation of cell population proliferation negative regulation of multicellular organismal process negative regulation of germ cell proliferation arachidonate metabolic process long-chain fatty acid metabolic process cyclooxygenase pathway olefinic compound metabolic process response to corticosteroid response to lipid response to hormone response to steroid hormone response to chemical response to endogenous stimulus response to glucocorticoid	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system extracellular region nuclear membrane membrane nucleus organelle envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system extracellular region nuclear membrane membrane nucleus organelle envelope nuclear envelope organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular space vesicle extracellular membrane-bounded organelle perinuclear region of cytoplasm rough endoplasmic reticulum endoplasmic reticulum organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012674	Calycin	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002345	Lipocalin	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000566	Lipocalin/cytosolic fatty-acid binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR022272	Lipocalin family conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	Pharos: P41222	medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm pituitary cancer adrenal cortex adenoma Sjogren syndrome atypical teratoid rhabdoid tumor chronic obstructive pulmonary disease glioblastoma large cell medulloblastoma lung cancer malignant mesothelioma non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm pituitary cancer adrenal cortex adenoma Sjogren syndrome atypical teratoid rhabdoid tumor chronic obstructive pulmonary disease glioblastoma large cell medulloblastoma lung cancer malignant mesothelioma non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor adrenal cortex carcinoma ulcerative colitis Becker muscular dystrophy Duchenne muscular dystrophy interstitial cystitis limb-girdle muscular dystrophy malignant ependymoma malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma schizophrenia atopic eczema bipolar disorder exocrine pancreatic carcinoma invasive ductal breast carcinoma lung adenocarcinoma malignant glioma

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.