1NKH

Crystal structure of Lactose synthase complex with UDP and Manganese

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1nkhb_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	beta 1,4 galactosyltransferase (b4GalT1)	beta 1,4 galactosyltransferase (b4GalT1)	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D	d1nkhd_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	beta 1,4 galactosyltransferase (b4GalT1)	beta 1,4 galactosyltransferase (b4GalT1)	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d1nkha_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	alpha-Lactalbumin	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d1nkhc_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	alpha-Lactalbumin	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8043892	3000077	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8043892	3000077	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lysozyme-like	8034893	3001879	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lysozyme-like	8034893	3001879	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	Glyco_transf_7N	e1nkhB1	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_7N	ECOD (1.6)
D	Glyco_transf_7N	e1nkhD1	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_7N	ECOD (1.6)
A	Lys	e1nkhA1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)
C	Lys	e1nkhC1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain 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)
A	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
C	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF02709	N-terminal domain of galactosyltransferase (Glyco_transf_7C)	N-terminal domain of galactosyltransferase	-	Family
B, D	PF13733	N-terminal region of glycosyl transferase group 7 (Glyco_transf_7N)	N-terminal region of glycosyl transferase group 7	This is the N-terminal half of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine syn ...	This is the N-terminal half of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalysed reaction.	Domain
A, C	PF00062	C-type lysozyme/alpha-lactalbumin family (Lys)	C-type lysozyme/alpha-lactalbumin family	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bac ...	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bacterial cell walls. Structure is a multi-domain, mixed alpha and beta fold, containing four conserved disulfide bonds.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	BETA-1,4-GALACTOSYLTRANSFERASE	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding cytoskeletal protein binding protein binding lactose synthase activity UDP-glycosyltransferase activity glycosyltransferase activity transferase activity galactosyltransferase activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding cytoskeletal protein binding protein binding lactose synthase activity UDP-glycosyltransferase activity glycosyltransferase activity transferase activity galactosyltransferase activity hexosyltransferase activity UDP-galactosyltransferase activity catalytic activity tubulin binding alpha-tubulin binding beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity beta-tubulin binding N-acetyllactosamine synthase activity identical protein binding	carbohydrate derivative biosynthetic process cellular biosynthetic process cellular metabolic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process protein glycosylation macromolecule biosynthetic process protein galactosylation biosynthetic process glycosylation macromolecule modification macromolecule glycosylation carbohydrate derivative biosynthetic process cellular biosynthetic process cellular metabolic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process protein glycosylation macromolecule biosynthetic process protein galactosylation biosynthetic process glycosylation macromolecule modification macromolecule glycosylation metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process lipid metabolic process biological regulation positive regulation of circulating fibrinogen levels regulation of biological quality regulation of circulating fibrinogen levels protein N-linked glycosylation carbohydrate metabolic process oligosaccharide biosynthetic process carbohydrate biosynthetic process oligosaccharide metabolic process disaccharide metabolic process lactose metabolic process disaccharide biosynthetic process lactose biosynthetic process	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane Golgi trans cisterna membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane Golgi trans cisterna membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle Golgi stack cytoplasm Golgi cisterna membrane organelle membrane basal part of cell basal plasma membrane plasma membrane region basolateral plasma membrane cell-cell junction anchoring junction desmosome cell junction brush border membrane cluster of actin-based cell projections plasma membrane bounded cell projection brush border cell projection cell projection membrane extracellular region extracellular space actin-based cell projection filopodium
A, C	ALPHA-LACTALBUMIN	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity lactose synthase activity UDP-glycosyltransferase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity lactose synthase activity UDP-glycosyltransferase activity glycosyltransferase activity transferase activity galactosyltransferase activity hexosyltransferase activity UDP-galactosyltransferase activity	carbohydrate metabolic process carbohydrate biosynthetic process oligosaccharide metabolic process primary metabolic process disaccharide metabolic process lactose metabolic process disaccharide biosynthetic process biosynthetic process oligosaccharide biosynthetic process metabolic process lactose biosynthetic process	extracellular region cellular anatomical entity protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR027995	Galactosyltransferase, N-terminal	Domain
B, D	IPR027791	Galactosyltransferase, C-terminal	Domain
B, D	IPR003859	Beta-1,4-galactosyltransferase	Family
B, D	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A, C	IPR001916	Glycoside hydrolase, family 22	Family
A, C	IPR019799	Glycoside hydrolase family 22 domain	Domain
A, C	IPR000545	Lactalbumin	Family
A, C	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily

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.