1YDG | pdb_00001ydg

Crystal Structure of Trp repressor binding protein WrbA

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	d1ydga1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	WrbA-like	Trp repressor binding protein WrbA	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
A	d1ydga2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
B	d1ydgb1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	WrbA-like	Trp repressor binding protein WrbA	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
B	d1ydgb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
C	d1ydgc1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	WrbA-like	Trp repressor binding protein WrbA	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
C	d1ydgc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
D	d1ydgd1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	WrbA-like	Trp repressor binding protein WrbA	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
D	d1ydgd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
E	d1ydge1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	WrbA-like	Trp repressor binding protein WrbA	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
E	d1ydge3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
E	d1ydge2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
F	d1ydgf1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	WrbA-like	Trp repressor binding protein WrbA	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
F	d1ydgf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
G	d1ydgg1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	WrbA-like	Trp repressor binding protein WrbA	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
G	d1ydgg2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
H	d1ydgh1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	WrbA-like	Trp repressor binding protein WrbA	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
H	d1ydgh2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	WrbA-like	8031921	4003377	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Flavoproteins	8044299	3001217	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Flavoproteins	8044299	3001217	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Flavoproteins	8044299	3001217	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Flavoproteins	8044299	3001217	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Flavoproteins	8044299	3001217	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Flavoproteins	8044299	3001217	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Flavoproteins	8044299	3001217	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Flavoproteins	8044299	3001217	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	Flavodoxin_1	e1ydgA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Flavoproteins	F: Flavodoxin_1	ECOD (v294.1)
B	B12-binding	e1ydgB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)
C	B12-binding	e1ydgC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)
D	B12-binding	e1ydgD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)
E	B12-binding	e1ydgE1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)
F	B12-binding	e1ydgF1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)
G	B12-binding	e1ydgG1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)
H	B12-binding	e1ydgH1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
B	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
C	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
D	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
E	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
F	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
G	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
H	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00258	Flavodoxin (Flavodoxin_1)	Flavodoxin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	trp repressor binding protein WrbA	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity NAD(P)H dehydrogenase (quinone) activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity NAD(P)H dehydrogenase (quinone) activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor catalytic activity NADPH dehydrogenase activity NADPH dehydrogenase (quinone) activity NADH dehydrogenase (quinone) (non-electrogenic) activity NADH dehydrogenase activity	-	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR010089	Flavoprotein WrbA-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029039	Flavoprotein-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR008254	Flavodoxin/nitric oxide synthase	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.