3K8D | pdb_00003k8d

Crystal structure of E. coli lipopolysaccharide specific CMP-KDO synthetase in complex with CTP and 2-deoxy-Kdo

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)
D	d3k8dd_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Cytidylytransferase	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d3k8dc_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Cytidylytransferase	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d3k8db_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Cytidylytransferase	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d3k8da_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Cytidylytransferase	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8035764	3000077	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8035764	3000077	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8035764	3000077	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8035764	3000077	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)
D	ATP-synt_ab_N	e3k8dD1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: ATP-synt_ab_N	ECOD (develop294)
C	ATP-synt_ab_N	e3k8dC1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: ATP-synt_ab_N	ECOD (develop294)
B	ATP-synt_ab_N	e3k8dB1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: ATP-synt_ab_N	ECOD (develop294)
A	RbsD_FucU	e3k8dA1	A: alpha bundles	X: Cystatin-like	H: NTF2-like	T: NTF2-like	F: RbsD_FucU	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain 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)
B	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain 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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02348	Cytidylyltransferase (CTP_transf_3)	Cytidylyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	3-deoxy-manno-octulosonate cytidylyltransferase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding cytidylyltransferase activity 3-deoxy-manno-octulosonate cytidylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	monosaccharide metabolic process lipopolysaccharide biosynthetic process oxoacid metabolic process lipid biosynthetic process carbohydrate derivative metabolic process organic acid biosynthetic process organic acid metabolic process keto-3-deoxy-D-manno-octulosonic acid biosynthetic process carboxylic acid biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process small molecule metabolic process carbohydrate derivative biosynthetic process carbohydrate metabolic process monosaccharide metabolic process lipopolysaccharide biosynthetic process oxoacid metabolic process lipid biosynthetic process carbohydrate derivative metabolic process organic acid biosynthetic process organic acid metabolic process keto-3-deoxy-D-manno-octulosonic acid biosynthetic process carboxylic acid biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process small molecule metabolic process carbohydrate derivative biosynthetic process carbohydrate metabolic process small molecule biosynthetic process polysaccharide biosynthetic process carbohydrate biosynthetic process liposaccharide metabolic process carboxylic acid metabolic process monosaccharide biosynthetic process primary metabolic process macromolecule biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process lipid metabolic process CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process nucleoside phosphate metabolic process nucleotide-sugar metabolic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process nucleotide-sugar biosynthetic process phosphorus metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004528	3-deoxy-D-manno-octulosonate cytidylyltransferase	Family
A, B, C, D	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A, B, C, D	IPR003329	Acylneuraminate cytidylyltransferase	Family

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.