3PDI

Precursor bound NifEN

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	d3pdia_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	automated matches	automated matches	(Azotobacter vinelandii DJ ) [TaxId: 322710 ],	SCOPe (2.08)
C	d3pdic_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	automated matches	automated matches	(Azotobacter vinelandii DJ ) [TaxId: 322710 ],	SCOPe (2.08)
E	d3pdie_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	automated matches	automated matches	(Azotobacter vinelandii DJ ) [TaxId: 322710 ],	SCOPe (2.08)
G	d3pdig_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	automated matches	automated matches	(Azotobacter vinelandii DJ ) [TaxId: 322710 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Helical backbone metal receptor	8097364	3001679	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Helical backbone metal receptor	8097364	3001679	SCOP2B (2022-06-29)
E	SCOP2 Family	Nitrogenase iron-molybdenum protein	8097363	4000849	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Helical backbone metal receptor	8097364	3001679	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	Helical backbone metal receptor	8097364	3001679	SCOP2B (2022-06-29)
B	SCOP2 Family	Nitrogenase iron-molybdenum protein	8076796	4000849	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Helical backbone metal receptor	8076797	3001679	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Helical backbone metal receptor	8076797	3001679	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Helical backbone metal receptor	8076797	3001679	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Helical backbone metal receptor	8076797	3001679	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	PF00148	e3pdiA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: PF00148	ECOD (1.6)
C	PF00148	e3pdiC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: PF00148	ECOD (1.6)
E	PF00148	e3pdiE2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: PF00148	ECOD (1.6)
G	PF00148	e3pdiG2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: PF00148	ECOD (1.6)
B	PF00148	e3pdiB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: PF00148	ECOD (1.6)
D	PF00148	e3pdiD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: PF00148	ECOD (1.6)
F	PF00148	e3pdiF2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: PF00148	ECOD (1.6)
H	PF00148	e3pdiH3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: PF00148	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
A	3.40.50.12380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase MoFe cofactor biosynthesis protein NifE, C-terminal	CATH (4.3.0)
C	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
C	3.40.50.12380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase MoFe cofactor biosynthesis protein NifE, C-terminal	CATH (4.3.0)
E	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
E	3.40.50.12380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase MoFe cofactor biosynthesis protein NifE, C-terminal	CATH (4.3.0)
G	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
G	3.40.50.12380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase MoFe cofactor biosynthesis protein NifE, C-terminal	CATH (4.3.0)
B	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
D	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
D	6.10.250.1090	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
F	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
F	6.10.250.1090	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
H	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
H	6.10.250.1090	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF00148	Nitrogenase component 1 type Oxidoreductase (Oxidored_nitro)	Nitrogenase component 1 type Oxidoreductase	-	Domain
B, D, F, H	PF00148	Nitrogenase component 1 type Oxidoreductase (Oxidored_nitro)	Nitrogenase component 1 type Oxidoreductase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	Nitrogenase MoFe cofactor biosynthesis protein NifE	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding oxidoreductase activity nitrogenase activity oxidoreductase activity, acting on iron-sulfur proteins as donors catalytic activity oxidoreductase activity, acting on iron-sulfur proteins as donors, dinitrogen as acceptor	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis nitrogen cycle metabolic process metabolic process nitrogen fixation	-
B, D, F, H	Nitrogenase MoFe cofactor biosynthesis protein NifN	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding oxidoreductase activity nitrogenase activity oxidoreductase activity, acting on iron-sulfur proteins as donors catalytic activity oxidoreductase activity, acting on iron-sulfur proteins as donors, dinitrogen as acceptor	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis nitrogen cycle metabolic process metabolic process nitrogen fixation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR000510	Nitrogenase/oxidoreductase, component 1	Domain
A, C, E, G	IPR005973	Nitrogenase MoFe cofactor biosynthesis protein NifE	Family
A, C, E, G	IPR000318	Nitrogenase component 1, conserved site	Conserved Site
B, D, F, H	IPR000510	Nitrogenase/oxidoreductase, component 1	Domain
B, D, F, H	IPR000318	Nitrogenase component 1, conserved site	Conserved Site
B, D, F, H	IPR005975	Nitrogenase molybdenum-iron cofactor biosynthesis protein	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 R01GM133198.