6NPF | pdb_00006npf

Structure of E.coli enolase in complex with an analog of the natural product SF-2312 metabolite.

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)
A	d6npfa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	Enolase	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d6npfa1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d6npfa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d6npfb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	Enolase	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d6npfb1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d6npfb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d6npfc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	Enolase	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d6npfc1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d6npfc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d6npfd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	Enolase	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d6npfd1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d6npfd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth E]	d6npfe2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	Enolase	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth E]	d6npfe1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth E]	d6npfe3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth F]	d6npff2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	Enolase	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth F]	d6npff1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth F]	d6npff3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
A	SCOP2B Superfamily	Enolase C-terminal domain-like	8041499	3000476	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Enolase N-terminal domain-like	8041500	3001064	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Enolase N-terminal domain-like	8041500	3001064	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Enolase C-terminal domain-like	8041499	3000476	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Enolase C-terminal domain-like	8041499	3000476	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Enolase N-terminal domain-like	8041500	3001064	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Enolase C-terminal domain-like	8041499	3000476	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Enolase N-terminal domain-like	8041500	3001064	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	Enolase C-terminal domain-like	8041499	3000476	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	Enolase N-terminal domain-like	8041500	3001064	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Enolase C-terminal domain-like	8041499	3000476	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Enolase N-terminal domain-like	8041500	3001064	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)
A	ATP-synt	e6npfA1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (develop294)
B	ATP-synt	e6npfB1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (develop294)
C	ATP-synt	e6npfC1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (develop294)
D	ATP-synt	e6npfD1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (develop294)
F [auth E]	ATP-synt	e6npfE1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (develop294)
E [auth F]	ATP-synt	e6npfF1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (utative)
A	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (utative)
B	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (utative)
B	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (utative)
C	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (utative)
C	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (utative)
D	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (utative)
D	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (utative)
F [auth E]	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (utative)
F [auth E]	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (utative)
E [auth F]	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (utative)
E [auth F]	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth E]	PF00113	Enolase, C-terminal TIM barrel domain (Enolase_C)	Enolase, C-terminal TIM barrel domain		Domain
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth E]	PF03952	Enolase, N-terminal domain (Enolase_N)	Enolase, N-terminal domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth E]	Enolase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding hydro-lyase activity lyase activity phosphopyruvate hydratase activity catalytic activity carbon-oxygen lyase activity identical protein binding protein binding protein homodimerization activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding hydro-lyase activity lyase activity phosphopyruvate hydratase activity catalytic activity carbon-oxygen lyase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration ATP metabolic process energy derivation by oxidation of organic compounds purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA processing	cellular anatomical structure membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle extracellular region bacterial degradosome exosome (RNase complex) protein-containing complex catalytic complex cytoplasm cellular anatomical structure membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle extracellular region bacterial degradosome exosome (RNase complex) protein-containing complex catalytic complex cytoplasm cytosol cytoplasmic exosome (RNase complex) exoribonuclease complex cell surface phosphopyruvate hydratase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth E]	IPR036849	Enolase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth E]	IPR020809	Enolase, conserved site	Conserved Site
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth E]	IPR020810	Enolase, C-terminal TIM barrel domain	Domain
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth E]	IPR020811	Enolase, N-terminal	Domain
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth E]	IPR000941	Enolase	Family
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth E]	IPR029017	Enolase-like, N-terminal	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.