2GP4

Structure of [FeS]cluster-free Apo Form of 6-Phosphogluconate Dehydratase from Shewanella oneidensis

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d2gp4a1	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	IlvD/EDD C-terminal domain-like	6-phosphogluconate dehydratase EDD	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)
A	d2gp4a2	Alpha and beta proteins (a+b)	IlvD/EDD N-terminal domain-like	IlvD/EDD N-terminal domain-like	lvD/EDD N-terminal domain-like	6-phosphogluconate dehydratase EDD	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)
A	d2gp4a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)
B	d2gp4b1	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	IlvD/EDD C-terminal domain-like	6-phosphogluconate dehydratase EDD	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)
B	d2gp4b2	Alpha and beta proteins (a+b)	IlvD/EDD N-terminal domain-like	IlvD/EDD N-terminal domain-like	lvD/EDD N-terminal domain-like	6-phosphogluconate dehydratase EDD	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)
B	d2gp4b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Shewanella oneidensis MR-1 ) [TaxId: 211586 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	lvD/EDD N-terminal domain-like	8029606	4000460	SCOP2 (2022-06-29)
A	SCOP2 Family	IlvD/EDD C-terminal domain-like	8029605	4002536	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	IlvD/EDD N-terminal domain-like	8041985	3000347	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LeuD/IlvD-like	8041984	3000947	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	LeuD/IlvD-like	8041984	3000947	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	PF00920	e2gp4A1	A: alpha arrays	X: lvD/EDD N-terminal domain-like (From Topology)	H: lvD/EDD N-terminal domain-like (From Topology)	T: lvD/EDD N-terminal domain-like	F: PF00920	ECOD (1.6)
A	PF00920	e2gp4A2	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF00920	ECOD (1.6)
B	PF00920	e2gp4B1	A: alpha arrays	X: lvD/EDD N-terminal domain-like (From Topology)	H: lvD/EDD N-terminal domain-like (From Topology)	T: lvD/EDD N-terminal domain-like	F: PF00920	ECOD (1.6)
B	PF00920	e2gp4B2	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF00920	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.50.30.80	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
B	3.50.30.80	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	6-phosphogluconate dehydratase	hydro-lyase activity lyase activity catalytic activity phosphogluconate dehydratase activity carbon-oxygen lyase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	catabolic process D-gluconate catabolic process oxoacid metabolic process carbohydrate catabolic process aldonic acid catabolic process organic acid metabolic process organic acid catabolic process cellular catabolic process organic substance metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process D-gluconate metabolic process small molecule metabolic process carbohydrate metabolic process catabolic process D-gluconate catabolic process oxoacid metabolic process carbohydrate catabolic process aldonic acid catabolic process organic acid metabolic process organic acid catabolic process cellular catabolic process organic substance metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process D-gluconate metabolic process small molecule metabolic process carbohydrate metabolic process cellular metabolic process carboxylic acid metabolic process primary metabolic process aldonic acid metabolic process metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process organic substance catabolic process Entner-Doudoroff pathway through 6-phosphogluconate carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process cellular aldehyde metabolic process phosphate-containing compound metabolic process Entner-Doudoroff pathway phosphorus metabolic process pyruvate metabolic process organophosphate metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004786	6-phosphogluconate dehydratase	Family
A, B	IPR000581	Dihydroxy-acid/6-phosphogluconate dehydratase	Family
A, B	IPR037237	IlvD/EDD, N-terminal domain	Homologous Superfamily
A, B	IPR042096	Dihydroxy-acid dehydratase, C-terminal	Homologous Superfamily
A, B	IPR020558	Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site	Conserved Site

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 R01GM133198.