1RYI | pdb_00001ryi

STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE

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)
D	d1ryid1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD-linked reductases, N-terminal domain	Glycine oxidase ThiO	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1ryid2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	D-aminoacid oxidase-like	Glycine oxidase ThiO	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1ryic1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD-linked reductases, N-terminal domain	Glycine oxidase ThiO	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1ryic2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	D-aminoacid oxidase-like	Glycine oxidase ThiO	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1ryib1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD-linked reductases, N-terminal domain	Glycine oxidase ThiO	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1ryib2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	D-aminoacid oxidase-like	Glycine oxidase ThiO	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1ryia1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD-linked reductases, N-terminal domain	Glycine oxidase ThiO	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1ryia2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	D-aminoacid oxidase-like	Glycine oxidase ThiO	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Flavoreductase-like	8057735	3000055	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Flavoreductase-like	8057735	3000055	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Flavoreductase-like	8057735	3000055	SCOP2B (2022-06-29)
A	SCOP2 Family	D-aminoacid oxidase-like	8057734	4000124	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Flavoreductase-like	8057735	3000055	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	YceM-like_C	e1ryiD1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
D		e1ryiD2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F:	ECOD (develop294)
C	YceM-like_C	e1ryiC1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
C		e1ryiC2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F:	ECOD (develop294)
B	YceM-like_C	e1ryiB1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
B		e1ryiB2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F:	ECOD (develop294)
A	DAO	e1ryiA1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C	T: FAD-linked reductases-C	F: DAO	ECOD (develop294)
A	DAO, NAD_binding_8	e1ryiA2	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: DAO, NAD_binding_8	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
D	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	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	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)
B	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
B	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	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	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01266	FAD dependent oxidoreductase (DAO)	FAD dependent oxidoreductase	This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	GLYCINE OXIDASE	FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding aliphatic amine oxidase activity oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity glycine oxidase activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding aliphatic amine oxidase activity oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity glycine oxidase activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor catalytic activity aliphatic amine dehydrogenase activity	pyrimidine-containing compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process thiamine diphosphate metabolic process sulfur compound metabolic process metabolic process pyrimidine-containing compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process thiamine diphosphate metabolic process sulfur compound metabolic process metabolic process cellular process small molecule metabolic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process thiamine diphosphate biosynthetic process thiamine-containing compound biosynthetic process alcohol metabolic process thiamine metabolic process thiamine biosynthetic process alcohol biosynthetic process primary alcohol biosynthetic process primary alcohol metabolic process response to stimulus response to chemical response to stress response to herbicide response to toxic substance amino acid metabolic process primary metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006076	FAD dependent oxidoreductase	Domain
A, B, C, D	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR012727	Glycine oxidase ThiO	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.