3GYX | pdb_00003gyx

Crystal structure of adenylylsulfate reductase from Desulfovibrio gigas

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L	Notch	e3gyxL1	A: alpha arrays	X: Transmembrane heme-binding four-helical bundle	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Notch	ECOD (v295)
J	Notch	e3gyxJ1	A: alpha arrays	X: Transmembrane heme-binding four-helical bundle	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Notch	ECOD (v295)
H	Notch	e3gyxH1	A: alpha arrays	X: Transmembrane heme-binding four-helical bundle	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Notch	ECOD (v295)
F	SNase	e3gyxF1	A: alpha arrays	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: SNase	ECOD (v295)
D	Notch	e3gyxD1	A: alpha arrays	X: Transmembrane heme-binding four-helical bundle	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Notch	ECOD (v295)
B	Notch	e3gyxB1	A: alpha arrays	X: Transmembrane heme-binding four-helical bundle	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Notch	ECOD (v295)
K	DNA_pol_B_exo1	e3gyxK3	A: alpha arrays	X: HAD domain-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_pol_B_exo1	ECOD (v295)
I	SET	e3gyxI3	A: alpha arrays	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: SET	ECOD (v295)
I	Sigma70_r2,Sigma70_ner	e3gyxI4	A: alpha arrays	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Sigma70_r2,Sigma70_ner	ECOD (v295)
G	SET	e3gyxG3	A: alpha arrays	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: SET	ECOD (v295)
G	DNA_pol_B_exo1	e3gyxG4	A: alpha arrays	X: HAD domain-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_pol_B_exo1	ECOD (v295)
E	SET	e3gyxE3	A: alpha arrays	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: SET	ECOD (v295)
E	DNA_pol_B_exo1	e3gyxE4	A: alpha arrays	X: HAD domain-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_pol_B_exo1	ECOD (v295)
C	SET	e3gyxC3	A: alpha arrays	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: SET	ECOD (v295)
C	Nup54_57_C	e3gyxC4	A: alpha arrays	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Nup54_57_C	ECOD (v295)
A	DNA_pol_B_exo1	e3gyxA4	A: alpha arrays	X: HAD domain-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_pol_B_exo1	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
L	6.20.260.10	Special	Other non-globular	Signal recognition particle alu RNA binding heterodimer, srp9/1	Adenylylsulphate reductase, beta subunit, C-terminal domain	CATH (4.3.0)
J	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
J	6.20.260.10	Special	Other non-globular	Signal recognition particle alu RNA binding heterodimer, srp9/1	Adenylylsulphate reductase, beta subunit, C-terminal domain	CATH (4.3.0)
H	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
H	6.20.260.10	Special	Other non-globular	Signal recognition particle alu RNA binding heterodimer, srp9/1	Adenylylsulphate reductase, beta subunit, C-terminal domain	CATH (4.3.0)
F	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
F	6.20.260.10	Special	Other non-globular	Signal recognition particle alu RNA binding heterodimer, srp9/1	Adenylylsulphate reductase, beta subunit, C-terminal domain	CATH (4.3.0)
D	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D	6.20.260.10	Special	Other non-globular	Signal recognition particle alu RNA binding heterodimer, srp9/1	Adenylylsulphate reductase, beta subunit, C-terminal domain	CATH (4.3.0)
B	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	6.20.260.10	Special	Other non-globular	Signal recognition particle alu RNA binding heterodimer, srp9/1	Adenylylsulphate reductase, beta subunit, C-terminal domain	CATH (4.3.0)
K	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
K	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)
I	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
I	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)
G	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
G	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)
E	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
E	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)
C	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
C	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L	PF12838	4Fe-4S dicluster domain (Fer4_7)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain
B, D, F, H, J B, D, F, H, J, L	PF12139	Adenosine-5'-phosphosulfate reductase beta subunit (APS-reductase_C)	Adenosine-5'-phosphosulfate reductase beta subunit	-	Family
A, C, E, G, I A, C, E, G, I, K	PF00890	FAD binding domain (FAD_binding_2)	FAD binding domain	This family includes members that bind FAD. This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L	Adenylylsulfate Reductase	protein heterodimerization activity protein binding binding protein dimerization activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	protein-containing complex organization protein heterotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein heterooligomerization cellular respiration dissimilatory sulfate reduction energy derivation by oxidation of organic compounds protein-containing complex organization protein heterotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein heterooligomerization cellular respiration dissimilatory sulfate reduction energy derivation by oxidation of organic compounds sulfate assimilation metabolic process sulfur compound metabolic process generation of precursor metabolites and energy anaerobic respiration	cellular anatomical structure intracellular anatomical structure cytoplasm
A, C, E, G, I A, C, E, G, I, K	Adenylylsulfate Reductase	oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding protein heterodimerization activity oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding protein heterodimerization activity protein binding protein dimerization activity oxidoreductase activity, acting on a sulfur group of donors adenylyl-sulfate reductase activity electron transfer activity	protein-containing complex organization protein heterotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein heterooligomerization cellular respiration dissimilatory sulfate reduction energy derivation by oxidation of organic compounds protein-containing complex organization protein heterotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein heterooligomerization cellular respiration dissimilatory sulfate reduction energy derivation by oxidation of organic compounds sulfate assimilation metabolic process sulfur compound metabolic process generation of precursor metabolites and energy anaerobic respiration	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B, D, F, H, J B, D, F, H, J, L	IPR038465	APS reductase, beta subunit, C-terminal domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR022738	Adenylylsulphate reductase, beta subunit, C-terminal	Domain
B, D, F, H, J B, D, F, H, J, L	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR011802	Adenylylsulphate reductase, beta subunit	Family
B, D, F, H, J B, D, F, H, J, L	IPR050572	Fe-S_Ferredoxin	Unknown
A, C, E, G, I A, C, E, G, I, K	IPR003953	FAD-dependent oxidoreductase 2, FAD-binding domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR037099	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR030664	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Family
A, C, E, G, I A, C, E, G, I, K	IPR011803	Adenylylsulphate reductase, alpha subunit	Family
A, C, E, G, I A, C, E, G, I, K	IPR027477	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Homologous Superfamily

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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.