3K1A | pdb_00003k1a

Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70Ile MoFe protein variant

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	d3k1aa_	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)
C	d3k1ac_	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)
B	d3k1ab_	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)
D	d3k1ad_	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)

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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Oxidored_nitro_3rd	e3k1aA1	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)
C	Oxidored_nitro_3rd	e3k1aC1	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_3rd	e3k1aB1	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	e3k1aB2	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	e3k1aB3	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)
D	Oxidored_nitro_3rd	e3k1aD3	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	e3k1aD2	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	e3k1aD1	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)

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 (4.2.0)
C	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	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)
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)

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

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 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
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 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
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	IPR050152	ChlB/BchB/BchZ	Family
B, D	IPR024564	Nitrogenase molybdenum-iron protein beta chain, N-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.