2AFH | pdb_00002afh

Crystal Structure of Nucleotide-Free Av2-Av1 Complex

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)
F	d2afhf_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nitrogenase iron protein-like	Nitrogenase iron protein	(Azotobacter vinelandii ) [TaxId: 354 ],	SCOPe (2.08)
E	d2afhe_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nitrogenase iron protein-like	Nitrogenase iron protein	(Azotobacter vinelandii ) [TaxId: 354 ],	SCOPe (2.08)
D	d2afhd_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	Nitrogenase iron-molybdenum protein	Nitrogenase iron-molybdenum protein, beta chain	(Azotobacter vinelandii ) [TaxId: 354 ],	SCOPe (2.08)
B	d2afhb_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	Nitrogenase iron-molybdenum protein	Nitrogenase iron-molybdenum protein, beta chain	(Azotobacter vinelandii ) [TaxId: 354 ],	SCOPe (2.08)
C	d2afhc_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	Nitrogenase iron-molybdenum protein	automated matches	(Azotobacter vinelandii ) [TaxId: 354 ],	SCOPe (2.08)
A	d2afha_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	Nitrogenase iron-molybdenum protein	automated matches	(Azotobacter vinelandii ) [TaxId: 354 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Simibi-like P-loop NTPases	8017762	3002018	SCOP2B (2022-06-29)
E	SCOP2 Family	NifH/FrxC-like	8017761	4003981	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Simibi-like P-loop NTPases	8017762	3002018	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Helical backbone metal receptor	8043192	3001679	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helical backbone metal receptor	8043192	3001679	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Helical backbone metal receptor	8043190	3001679	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helical backbone metal receptor	8043190	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)
F	AAA_31	e2afhF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_31	ECOD (1.6)
E	AAA_31	e2afhE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_31	ECOD (1.6)
D	Oxidored_nitro_3rd	e2afhD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: Oxidored_nitro_3rd	ECOD (1.6)
D	Oxidored_nitro_1st	e2afhD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: Oxidored_nitro_1st	ECOD (1.6)
D	UNK_F_TYPE	e2afhD3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: UNK_F_TYPE	ECOD (1.6)
B	Oxidored_nitro_3rd	e2afhB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: Oxidored_nitro_3rd	ECOD (1.6)
B	Oxidored_nitro_1st	e2afhB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: Oxidored_nitro_1st	ECOD (1.6)
B	UNK_F_TYPE	e2afhB3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: UNK_F_TYPE	ECOD (1.6)
C	Oxidored_nitro_3rd	e2afhC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: Oxidored_nitro_3rd	ECOD (1.6)
A	Oxidored_nitro_3rd	e2afhA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: Oxidored_nitro_3rd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)
D	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.2.0)
D	1.20.89.10	Mainly Alpha	Up-down Bundle	Nitrogenase Molybdenum-iron Protein, subunit B	domain 4	CATH (4.2.0)
B	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.2.0)
B	1.20.89.10	Mainly Alpha	Up-down Bundle	Nitrogenase Molybdenum-iron Protein, subunit B	domain 4	CATH (4.2.0)
C	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.2.0)
A	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	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 anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation 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	nitrogen cycle metabolic process metabolic process cellular process nitrogen fixation	-
B, D	Nitrogenase molybdenum-iron protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 cation 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	nitrogen cycle metabolic process metabolic process cellular process nitrogen fixation	protein-containing complex molybdenum-iron nitrogenase complex catalytic complex nitrogenase complex oxidoreductase complex intracellular protein-containing complex
A, C	Nitrogenase molybdenum-iron protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 cation 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	nitrogen cycle metabolic process metabolic process cellular process nitrogen fixation	protein-containing complex molybdenum-iron nitrogenase complex catalytic complex nitrogenase complex oxidoreductase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR030655	NifH/chlL conserved site	Conserved Site
E, F	IPR000392	NifH/frxC family	Family
E, F	IPR005977	Nitrogenase iron protein NifH	Family
E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
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	IPR050152	ChlB/BchB/BchZ	Family
B, D	IPR024564	Nitrogenase molybdenum-iron protein beta chain, N-terminal	Domain
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

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.