4D0Z | pdb_00004d0z

GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 and manganese (Higher resolution dataset)

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	PemK_toxin	e4d0zF2	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
F	Iso_dh	e4d0zF1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Iso_dh	ECOD (v294.1)
E	PemK_toxin	e4d0zE2	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
E	Iso_dh	e4d0zE1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Iso_dh	ECOD (v294.1)
D	PemK_toxin	e4d0zD2	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
D	Iso_dh	e4d0zD3	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Iso_dh	ECOD (v294.1)
C	PemK_toxin	e4d0zC2	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
C	Iso_dh	e4d0zC3	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Iso_dh	ECOD (v294.1)
B	PemK_toxin	e4d0zB2	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
B	Iso_dh	e4d0zB1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Iso_dh	ECOD (v294.1)
A	PemK_toxin	e4d0zA2	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
A	Iso_dh	e4d0zA3	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Iso_dh	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
F	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
E	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
E	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
D	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
D	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
C	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
C	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
B	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
B	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
A	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
A	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		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	PF00535	Glycosyl transferase family 2 (Glycos_transf_2)	Glycosyl transferase family 2	Diverse family, transferring sugar from UDP-glucose, UDP-N-acetyl- galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids.	Domain
A, B, C, D, E A, B, C, D, E, F	PF00652	Ricin-type beta-trefoil lectin domain (Ricin_B_lectin)	Ricin-type beta-trefoil lectin domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth X], H [auth Y]	PEPTIDE	extracellular matrix binding binding protein binding growth factor binding cell adhesion molecule binding protein-containing complex binding integrin binding signaling receptor binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation labyrinthine layer blood vessel development placenta blood vessel development placenta development chordate embryonic development animal organ development labyrinthine layer development embryo development developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation labyrinthine layer blood vessel development placenta blood vessel development placenta development chordate embryonic development animal organ development labyrinthine layer development embryo development in utero embryonic development vasculature development circulatory system development multicellular organism development embryonic placenta development embryo development ending in birth or egg hatching anatomical structure development embryonic organ development blood vessel development system development heart development ventricular septum development cardiac septum development cardiac chamber development cardiac ventricle development cardiac atrium morphogenesis cardiac chamber morphogenesis heart morphogenesis cardiac atrium development anatomical structure morphogenesis cardiac septum morphogenesis atrial septum morphogenesis animal organ morphogenesis atrial septum development reactive oxygen species metabolic process metabolic process regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion positive regulation of biological process cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion positive regulation of cellular process cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization cellular response to stimulus integrin-mediated signaling pathway cell surface receptor signaling pathway response to stimulus signaling cell communication signal transduction positive regulation of programmed cell death positive regulation of apoptotic process connective tissue development tissue development chondroblast differentiation skeletal system development cartilage development apoptotic process involved in heart morphogenesis apoptotic process involved in morphogenesis apoptotic process involved in development regulation of developmental process regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of developmental process positive regulation of biomineral tissue development biomineral tissue development regulation of multicellular organismal process regulation of multicellular organismal development bone mineralization positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification regulation of cell differentiation positive regulation of cell differentiation positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway positive regulation of signal transduction cellular response to growth factor stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of signal transduction positive regulation of BMP signaling pathway positive regulation of response to stimulus cellular response to endogenous stimulus BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of signaling regulation of BMP signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway response to BMP regulation of response to stimulus regulation of cell communication transforming growth factor beta receptor superfamily signaling pathway response to growth factor positive regulation of signaling chemotaxis taxis response to chemical response to external stimulus locomotion 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 embryonic morphogenesis chorio-allantoic fusion embryonic placenta morphogenesis labyrinthine layer morphogenesis cell-cell adhesion regulation of osteoblast differentiation positive regulation of osteoblast differentiation blood vessel morphogenesis tube development angiogenesis tube morphogenesis anatomical structure formation involved in morphogenesis intussusceptive angiogenesis positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility regulation of MAPK cascade intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process regulation of cartilage development positive regulation of cartilage development atrioventricular valve development heart valve development heart valve morphogenesis atrioventricular valve morphogenesis sphingolipid biosynthetic process regulation of lipid metabolic process positive regulation of ceramide biosynthetic process lipid biosynthetic process positive regulation of sphingolipid biosynthetic process cellular component biogenesis regulation of sphingolipid biosynthetic process positive regulation of lipid metabolic process regulation of ceramide biosynthetic process ceramide metabolic process sphingolipid metabolic process regulation of cellular component biogenesis positive regulation of lipid biosynthetic process ceramide biosynthetic process regulation of lipid biosynthetic process lipid metabolic process	cell periphery extracellular matrix cellular anatomical structure external encapsulating structure membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle cell periphery extracellular matrix cellular anatomical structure external encapsulating structure membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region extracellular space
A, B, C, D, E A, B, C, D, E, F	POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2	binding carbohydrate binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding UDP-glycosyltransferase activity polypeptide N-acetylgalactosaminyltransferase activity catalytic activity, acting on a protein glycosyltransferase activity transferase activity acetylgalactosaminyltransferase activity binding carbohydrate binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding UDP-glycosyltransferase activity polypeptide N-acetylgalactosaminyltransferase activity catalytic activity, acting on a protein glycosyltransferase activity transferase activity acetylgalactosaminyltransferase activity hexosyltransferase activity catalytic activity	carbohydrate derivative biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process macromolecule biosynthetic process biosynthetic process protein O-linked glycosylation metabolic process cellular process protein O-linked glycosylation via N-acetyl-galactosamine protein metabolic process macromolecule metabolic process regulation of immune effector process carbohydrate derivative biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process macromolecule biosynthetic process biosynthetic process protein O-linked glycosylation metabolic process cellular process protein O-linked glycosylation via N-acetyl-galactosamine protein metabolic process macromolecule metabolic process regulation of immune effector process regulation of cellular process immunoglobulin production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of immune effector process regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of immune system process positive regulation of cellular process positive regulation of immunoglobulin production regulation of biosynthetic process production of molecular mediator of immune response regulation of biological process biological regulation regulation of macromolecule metabolic process gene expression immune effector process regulation of gene expression regulation of immunoglobulin production positive regulation of gene expression immune system process positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process regulation of production of molecular mediator of immune response regulation of metabolic process protein maturation	membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle Golgi stack cytoplasm membrane extracellular region membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle Golgi stack cytoplasm membrane extracellular region Golgi membrane bounding membrane of organelle organelle membrane Golgi cisterna membrane Golgi cisterna perinuclear region of cytoplasm 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
G [auth X], H [auth Y]	IPR012395	IGFBP-related, CNN	Family
G [auth X], H [auth Y]	IPR001007	VWFC domain	Domain
G [auth X], H [auth Y]	IPR000867	Insulin-like growth factor-binding protein, IGFBP	Domain
G [auth X], H [auth Y]	IPR043973	CCN, TSP1 domain	Domain
G [auth X], H [auth Y]	IPR000884	Thrombospondin type-1 (TSP1) repeat	Repeat
G [auth X], H [auth Y]	IPR050941	Cellular Communication Network Factor	Family
G [auth X], H [auth Y]	IPR036383	Thrombospondin type-1 repeat superfamily	Homologous Superfamily
G [auth X], H [auth Y]	IPR006208	Glycoprotein hormone subunit beta	Domain
G [auth X], H [auth Y]	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
G [auth X], H [auth Y]	IPR006207	Cystine knot, C-terminal	Domain
G [auth X], H [auth Y]	IPR017891	Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR045885	N-acetylgalactosaminyltransferase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR035992	Ricin B-like lectins	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001173	Glycosyltransferase 2-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000772	Ricin B, lectin domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
G [auth X], H [auth Y]	Pharos: O00622	rheumatoid arthritis Lung Neoplasms malignant pancreatic neoplasm nephrosclerosis ovarian cancer adrenal cortex carcinoma pancreatic intraductal papillary-mucinous neoplasm breast cancer pituitary cancer diabetes mellitus sarcoidosis gastric carcinoma subependymal giant cell astrocytoma interstitial cystitis lung cancer rheumatoid arthritis Lung Neoplasms malignant pancreatic neoplasm nephrosclerosis ovarian cancer adrenal cortex carcinoma pancreatic intraductal papillary-mucinous neoplasm breast cancer pituitary cancer diabetes mellitus sarcoidosis gastric carcinoma subependymal giant cell astrocytoma interstitial cystitis lung cancer malignant ependymoma medulloblastoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma amyotrophic lateral sclerosis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast carcinoma psoriasis Emery-Dreifuss muscular dystrophy Sjogren syndrome glioblastoma ulcerative colitis juvenile dermatomyositis lung adenocarcinoma lung carcinoma myopathy osteosarcoma pancreatic intraductal papillary-mucinous carcinoma atypical teratoid rhabdoid tumor periodontitis cystic fibrosis facioscapulohumeral muscular dystrophy spina bifida hepatocellular carcinoma limb-girdle muscular dystrophy lung benign neoplasm
A, B, C, D, E A, B, C, D, E, F	Pharos: Q10471	metabolic syndrome X pancreatic ductal adenocarcinoma pilocytic astrocytoma astrocytic tumor breast carcinoma diabetes mellitus lung adenocarcinoma malignant ependymoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma atypical teratoid rhabdoid tumor congenital disorder of glycosylation gastric carcinoma lung cancer metabolic syndrome X pancreatic ductal adenocarcinoma pilocytic astrocytoma astrocytic tumor breast carcinoma diabetes mellitus lung adenocarcinoma malignant ependymoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma atypical teratoid rhabdoid tumor congenital disorder of glycosylation gastric carcinoma lung cancer malignant glioma non-small cell lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis breast cancer Crohn disease glioblastoma lymphoplasmacytic lymphoma malignant mesothelioma oligodendroglioma

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.