2GP4 | pdb_00002gp4

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	IlvD/EDD C-terminal domain-like	8029605	4002536	SCOP2 (2022-06-29)
A	SCOP2 Family	lvD/EDD N-terminal domain-like	8029606	4000460	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LeuD/IlvD-like	8041984	3000947	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	IlvD/EDD N-terminal domain-like	8041985	3000347	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	ILVD_EDD_1st	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: ILVD_EDD_1st	ECOD (1.6)
A	ILVD_EDD_2nd	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: ILVD_EDD_2nd	ECOD (1.6)
B	ILVD_EDD_1st	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: ILVD_EDD_1st	ECOD (1.6)
B	ILVD_EDD_2nd	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: ILVD_EDD_2nd	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	Entner-Doudoroff pathway through 6-phosphogluconate carbohydrate metabolic process pyruvate metabolic process catabolic process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process carboxylic acid metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process organic acid metabolic process aldehyde metabolic process organophosphate metabolic process phosphate-containing compound metabolic process Entner-Doudoroff pathway through 6-phosphogluconate carbohydrate metabolic process pyruvate metabolic process catabolic process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process carboxylic acid metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process organic acid metabolic process aldehyde metabolic process organophosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process Entner-Doudoroff pathway monocarboxylic acid metabolic process phosphorus metabolic process D-gluconate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm 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, N-terminal	Domain
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
A, B	IPR056740	Dihydroxy-acid/6-phosphogluconate dehydratase, C-terminal	Domain

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.