3ND5 | pdb_00003nd5

Crystal structure of phosphopantetheine adenylyltransferase (PPAT) from Enterococcus faecalis

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)
F	d3nd5f_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	Streptococcus faecalis (Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
E	d3nd5e_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	Streptococcus faecalis (Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
D	d3nd5d_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	Streptococcus faecalis (Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
C	d3nd5c_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	Streptococcus faecalis (Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
B	d3nd5b_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	Streptococcus faecalis (Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
A	d3nd5a_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	Streptococcus faecalis (Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Nucleotidylyl transferase	8064675	3001541	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleotidylyl transferase	8064675	3001541	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotidylyl transferase	8064675	3001541	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotidylyl transferase	8064675	3001541	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotidylyl transferase	8064675	3001541	SCOP2B (2022-06-29)
A	SCOP2 Family	Adenylyltransferase	8064674	4003834	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotidylyl transferase	8064675	3001541	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	YjeF_N	e3nd5F1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (develop294)
E	YjeF_N	e3nd5E1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (develop294)
D	YjeF_N	e3nd5D1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (develop294)
C	YjeF_N	e3nd5C1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (develop294)
B	YjeF_N	e3nd5B1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (develop294)
A	TIM	e3nd5A1	A: alpha bundles	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: TIM	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
E	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
D	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
C	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	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	PF01467	Cytidylyltransferase-like (CTP_transf_like)	Cytidylyltransferase-like	This family includes: Cholinephosphate cytidylyltransferase Swiss:P49585; glycerol-3-phosphate cytidylyltransferase Swiss:P27623. It also includes putative adenylyltransferases, and FAD synthases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Phosphopantetheine adenylyltransferase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pantetheine-phosphate adenylyltransferase activity adenylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	nucleoside phosphate metabolic process coenzyme A biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process coenzyme A biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process phosphorus metabolic process coenzyme A metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR004821	Cytidyltransferase-like domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001980	Phosphopantetheine adenylyltransferase	Family
A, B, C, D, E A, B, C, D, E, F	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.