4WMI | pdb_00004wmi

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex I)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B [auth D]	d4wmid_	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	EGF-type module	Factor IX (IXa)	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)
B [auth D]	SCOP2B Superfamily	EGF/Laminin-like	8038255	3000412	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)
B [auth D]	hEGF	e4wmiD1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: hEGF	ECOD (1.6)
A	Glyco_transf_8	e4wmiA1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: Glyco_transf_8	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D]	PF00008	EGF-like domain (EGF)	EGF-like domain	There is no clear separation between noise and signal. Pfam:PF00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is t ...	There is no clear separation between noise and signal. Pfam:PF00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.	Domain
A	PF01501	Glycosyl transferase family 8 (Glyco_transf_8)	Glycosyl transferase family 8	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D]	Coagulation factor IX	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding proteolysis metabolic process cellular process multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process zymogen activation gene expression macromolecule biosynthetic process protein maturation biosynthetic process protein processing	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane intracellular anatomical structure extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen cytoplasm endoplasmic reticulum lumen endoplasmic reticulum
A	Xyloside xylosyltransferase 1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding xylosyltransferase activity UDP-glycosyltransferase activity pentosyltransferase activity glycosyltransferase activity xylosyl alpha-1,3-xylosyltransferase activity transferase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding xylosyltransferase activity UDP-glycosyltransferase activity pentosyltransferase activity glycosyltransferase activity xylosyl alpha-1,3-xylosyltransferase activity transferase activity UDP-xylosyltransferase 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	membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
B [auth D]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B [auth D]	IPR000742	EGF-like domain	Domain
B [auth D]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
B [auth D]	IPR050442	Peptidase S1 family, coagulation factors	Family
B [auth D]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B [auth D]	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
B [auth D]	IPR001314	Peptidase S1A, chymotrypsin family	Family
B [auth D]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
B [auth D]	IPR001254	Serine proteases, trypsin domain	Domain
B [auth D]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
B [auth D]	IPR001881	EGF-like calcium-binding domain	Domain
B [auth D]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B [auth D]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
B [auth D]	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family
A	IPR002495	Glycosyl transferase, family 8	Family
A	IPR042465	Xyloside xylosyltransferase 1	Family
A	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth D]	Pharos: P00740	hemophilia B hemophilia A thrombophilia, X-linked, due to factor 9 defect coumarin resistance malignant mesothelioma thrombophilia thrombotic disease Autosomal Hemophilia A hemophilia bipolar disorder psoriasis vascular disease congenital factor XI deficiency

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.