3PDI | pdb_00003pdi

Precursor bound NifEN

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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	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)
D	SCOP2B Superfamily	Helical backbone metal receptor	8076797	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)
C	SCOP2B Superfamily	Helical backbone metal receptor	8097364	3001679	SCOP2B (2022-06-29)
G	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)
A	SCOP2B Superfamily	Helical backbone metal receptor	8097364	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)
H	PrpR_N	e3pdiH1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: PrpR_N	ECOD (v294.1)
F	PrpR_N	e3pdiF1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: PrpR_N	ECOD (v294.1)
D	PrpR_N	e3pdiD1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: PrpR_N	ECOD (v294.1)
B	PrpR_N	e3pdiB1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: PrpR_N	ECOD (v294.1)
C	PrpR_N	e3pdiC1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: PrpR_N	ECOD (v294.1)
G	PrpR_N	e3pdiG1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: PrpR_N	ECOD (v294.1)
E	PrpR_N	e3pdiE1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: PrpR_N	ECOD (v294.1)
A	PrpR_N	e3pdiA1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: PrpR_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
B	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
C	3.40.50.1980	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)
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)
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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	-
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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR050152	ChlB/BchB/BchZ	Family
B, D, F, H	IPR005975	Nitrogenase molybdenum-iron cofactor biosynthesis protein	Family
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
A, C, E, G	IPR049939	Nitrogenase MoFe cofactor biosynthesis protein NifE-like	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.