6ZDM | pdb_00006zdm

Crystal structure of human heparanase in complex with a N',6O'-bis-sulfated 4-methylumbelliferyl heparan sulfate disaccharide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth BBB]	SCOP2B Superfamily	(Trans)glycosidases	8051984	3000313	SCOP2B (2022-06-29)
B [auth BBB]	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8051986	3001528	SCOP2B (2022-06-29)
A [auth AAA]	SCOP2B Superfamily	(Trans)glycosidases	8051984	3000313	SCOP2B (2022-06-29)
A [auth AAA]	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8051986	3001528	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)
A [auth AAA]	WD40	e6zdmAAA1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: WD40	ECOD (v295.2)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth BBB]	Heparanase	hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds beta-glucuronidase activity glucuronidase activity hydrolase activity catalytic activity protein binding binding syndecan binding proteoglycan binding carbohydrate derivative binding heparanase activity	cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process carbohydrate derivative metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process proteoglycan metabolic process glycoprotein metabolic process multicellular organismal process regulation of cellular process positive regulation of biological process cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process carbohydrate derivative metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process proteoglycan metabolic process glycoprotein metabolic process multicellular organismal process regulation of cellular process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression vascular endothelial growth factor production biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of vascular endothelial growth factor production regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process response to stimulus response to chemical response to antibiotic heparin proteoglycan metabolic process cellular response to stimulus positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling cell population proliferation positive regulation of cell population proliferation positive regulation of osteoblast proliferation osteoblast proliferation regulation of cell population proliferation regulation of osteoblast proliferation transmembrane transport localization establishment of protein localization protein transmembrane transport transport protein transport macromolecule localization intracellular protein localization establishment of localization regulation of developmental process epidermis development molting cycle process regulation of hair cycle positive regulation of developmental process multicellular organism development skin epidermis development hair follicle development anatomical structure development developmental process epithelium development regulation of multicellular organismal development hair cycle animal organ development tissue development positive regulation of hair follicle development skin development molting cycle regulation of hair follicle development hair cycle process animal gross anatomical part developmental process endothelial cell differentiation cellular developmental process endothelium development cell development epithelial cell differentiation endothelial cell development epithelial cell development cell differentiation establishment of endothelial barrier wound healing blood vessel morphogenesis tube development angiogenesis involved in wound healing angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis vascular wound healing response to stress anatomical structure formation involved in morphogenesis response to wounding blood vessel development system development carbohydrate derivative catabolic process glycoprotein catabolic process catabolic process heparan sulfate proteoglycan metabolic process protein catabolic process macromolecule catabolic process heparan sulfate proteoglycan catabolic process proteoglycan catabolic process regulation of body fluid levels positive regulation of coagulation regulation of response to external stimulus positive regulation of blood coagulation regulation of response to wounding regulation of coagulation regulation of response to stress coagulation positive regulation of hemostasis regulation of biological quality regulation of hemostasis positive regulation of response to wounding regulation of blood coagulation hemostasis response to external stimulus blood coagulation positive regulation of wound healing regulation of wound healing	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm lysosome cell periphery plasma membrane membrane membrane microdomain membrane raft extracellular matrix external encapsulating structure extracellular region nucleus nucleoplasm nuclear lumen vacuolar membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane vesicle lumen intracellular vesicle cytoplasmic vesicle lumen secretory granule lumen endomembrane system cytoplasmic vesicle specific granule lumen secretory granule secretory vesicle vesicle specific granule
A [auth AAA]	Heparanase	hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds beta-glucuronidase activity glucuronidase activity hydrolase activity catalytic activity protein binding binding syndecan binding proteoglycan binding carbohydrate derivative binding heparanase activity	cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process carbohydrate derivative metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process proteoglycan metabolic process glycoprotein metabolic process multicellular organismal process regulation of cellular process positive regulation of biological process cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process carbohydrate derivative metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process proteoglycan metabolic process glycoprotein metabolic process multicellular organismal process regulation of cellular process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression vascular endothelial growth factor production biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of vascular endothelial growth factor production regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process response to stimulus response to chemical response to antibiotic heparin proteoglycan metabolic process cellular response to stimulus positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling cell population proliferation positive regulation of cell population proliferation positive regulation of osteoblast proliferation osteoblast proliferation regulation of cell population proliferation regulation of osteoblast proliferation transmembrane transport localization establishment of protein localization protein transmembrane transport transport protein transport macromolecule localization intracellular protein localization establishment of localization regulation of developmental process epidermis development molting cycle process regulation of hair cycle positive regulation of developmental process multicellular organism development skin epidermis development hair follicle development anatomical structure development developmental process epithelium development regulation of multicellular organismal development hair cycle animal organ development tissue development positive regulation of hair follicle development skin development molting cycle regulation of hair follicle development hair cycle process animal gross anatomical part developmental process endothelial cell differentiation cellular developmental process endothelium development cell development epithelial cell differentiation endothelial cell development epithelial cell development cell differentiation establishment of endothelial barrier wound healing blood vessel morphogenesis tube development angiogenesis involved in wound healing angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis vascular wound healing response to stress anatomical structure formation involved in morphogenesis response to wounding blood vessel development system development carbohydrate derivative catabolic process glycoprotein catabolic process catabolic process heparan sulfate proteoglycan metabolic process protein catabolic process macromolecule catabolic process heparan sulfate proteoglycan catabolic process proteoglycan catabolic process regulation of body fluid levels positive regulation of coagulation regulation of response to external stimulus positive regulation of blood coagulation regulation of response to wounding regulation of coagulation regulation of response to stress coagulation positive regulation of hemostasis regulation of biological quality regulation of hemostasis positive regulation of response to wounding regulation of blood coagulation hemostasis response to external stimulus blood coagulation positive regulation of wound healing regulation of wound healing	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm lysosome cell periphery plasma membrane membrane membrane microdomain membrane raft extracellular matrix external encapsulating structure extracellular region nucleus nucleoplasm nuclear lumen vacuolar membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane vesicle lumen intracellular vesicle cytoplasmic vesicle lumen secretory granule lumen endomembrane system cytoplasmic vesicle specific granule lumen secretory granule secretory vesicle vesicle specific granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth BBB]	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
B [auth BBB]	IPR005199	Glycoside hydrolase, family 79	Family
A [auth AAA]	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A [auth AAA]	IPR005199	Glycoside hydrolase, family 79	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth BBB]	: Q9Y251	IgA glomerulonephritis melanoma Neoplasm Metastasis nephrosis breast carcinoma MALT lymphoma medulloblastoma ovarian cancer adrenal cortex carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Crohn disease subependymal giant cell astrocytoma depressive disorder large cell medulloblastoma major depressive disorder IgA glomerulonephritis melanoma Neoplasm Metastasis nephrosis breast carcinoma MALT lymphoma medulloblastoma ovarian cancer adrenal cortex carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Crohn disease subependymal giant cell astrocytoma depressive disorder large cell medulloblastoma major depressive disorder pancreatic intraductal papillary-mucinous carcinoma breast cancer psoriasis cutaneous lupus erythematosus ulcerative colitis interstitial cystitis malignant glioma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm Sjogren syndrome cutaneous melanoma glioblastoma invasive ductal breast carcinoma malignant mesothelioma
A [auth AAA]	: Q9Y251	IgA glomerulonephritis melanoma Neoplasm Metastasis nephrosis breast carcinoma MALT lymphoma medulloblastoma ovarian cancer adrenal cortex carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Crohn disease subependymal giant cell astrocytoma depressive disorder large cell medulloblastoma major depressive disorder IgA glomerulonephritis melanoma Neoplasm Metastasis nephrosis breast carcinoma MALT lymphoma medulloblastoma ovarian cancer adrenal cortex carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Crohn disease subependymal giant cell astrocytoma depressive disorder large cell medulloblastoma major depressive disorder pancreatic intraductal papillary-mucinous carcinoma breast cancer psoriasis cutaneous lupus erythematosus ulcerative colitis interstitial cystitis malignant glioma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm Sjogren syndrome cutaneous melanoma glioblastoma invasive ductal breast carcinoma malignant mesothelioma

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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.