8DFD

CryoEM structure of the 2:1 ADP-tetrafluoroaluminate stabilized nitrogenase complex from Azotobacter vinelandii

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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	8043190	3001679	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Helical backbone metal receptor	8043190	3001679	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helical backbone metal receptor	8043192	3001679	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Helical backbone metal receptor	8043192	3001679	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Simibi-like P-loop NTPases	8017762	3002018	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Simibi-like P-loop NTPases	8017762	3002018	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Simibi-like P-loop NTPases	8017762	3002018	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Simibi-like P-loop NTPases	8017762	3002018	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	e8dfdA1	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	e8dfdC3	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	e8dfdB2	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,PF11844	e8dfdB3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: PF00148,PF11844	ECOD (1.6)
D	PF00148	e8dfdD3	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,PF11844	e8dfdD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: PF00148,PF11844	ECOD (1.6)
E	PF00142	e8dfdE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00142	ECOD (1.6)
F	PF00142	e8dfdF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00142	ECOD (1.6)
G	PF00142	e8dfdG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00142	ECOD (1.6)
H	PF00142	e8dfdH1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00142	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00148	Nitrogenase component 1 type Oxidoreductase (Oxidored_nitro)	Nitrogenase component 1 type Oxidoreductase	-	Domain
B, D	PF11844	Domain of unknown function (DUF3364) (DUF3364)	Domain of unknown function (DUF3364)	-	Family
B, D	PF00148	Nitrogenase component 1 type Oxidoreductase (Oxidored_nitro)	Nitrogenase component 1 type Oxidoreductase	-	Domain
E, F, G, H	PF00142	4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family (Fer4_NifH)	4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Nitrogenase molybdenum-iron protein alpha chain	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding iron-sulfur cluster binding metal cluster binding oxidoreductase activity oxidoreductase activity, acting on iron-sulfur proteins as donors catalytic activity carbonyl sulfide nitrogenase activity oxidoreductase activity, acting on iron-sulfur proteins as donors, dinitrogen as acceptor cation binding metal ion binding nitrogenase activity	nitrogen cycle metabolic process metabolic process nitrogen fixation	protein-containing complex molybdenum-iron nitrogenase complex catalytic complex nitrogenase complex oxidoreductase complex intracellular protein-containing complex
B, D	Nitrogenase molybdenum-iron protein beta chain	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding iron-sulfur cluster binding metal cluster binding oxidoreductase activity oxidoreductase activity, acting on iron-sulfur proteins as donors catalytic activity carbonyl sulfide nitrogenase activity oxidoreductase activity, acting on iron-sulfur proteins as donors, dinitrogen as acceptor cation binding metal ion binding nitrogenase activity	nitrogen cycle metabolic process metabolic process nitrogen fixation	protein-containing complex molybdenum-iron nitrogenase complex catalytic complex nitrogenase complex oxidoreductase complex intracellular protein-containing complex
E, F, G, H	Nitrogenase iron protein 1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on iron-sulfur proteins as donors catalytic activity carbonyl sulfide nitrogenase activity oxidoreductase activity, acting on iron-sulfur proteins as donors, dinitrogen as acceptor iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding nitrogenase activity	nitrogen cycle metabolic process metabolic process nitrogen fixation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR000510	Nitrogenase/oxidoreductase, component 1	Domain
A, C	IPR005972	Nitrogenase molybdenum-iron protein alpha chain	Family
A, C	IPR000318	Nitrogenase component 1, conserved site	Conserved Site
A, C	IPR010143	Nitrogenase component 1, alpha chain	Family
B, D	IPR000510	Nitrogenase/oxidoreductase, component 1	Domain
B, D	IPR005976	Nitrogenase molybdenum-iron protein beta chain	Family
B, D	IPR000318	Nitrogenase component 1, conserved site	Conserved Site
B, D	IPR024564	Nitrogenase molybdenum-iron protein beta chain, N-terminal	Domain
E, F, G, H	IPR030655	NifH/chlL conserved site	Conserved Site
E, F, G, H	IPR000392	NifH/frxC family	Family
E, F, G, H	IPR005977	Nitrogenase iron protein NifH	Family
E, F, G, H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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 R01GM133198.