3GDP

Hydroxynitrile lyase from almond, monoclinic crystal form

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Flavoreductase-like	8058154	3000055	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Flavoreductase-like	8058154	3000055	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)
B	GMC_oxred_C	e3gdpB1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: GMC_oxred_C	ECOD (1.6)
B	GMC_oxred_N	e3gdpB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: GMC_oxred_N	ECOD (1.6)
A	GMC_oxred_C	e3gdpA1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: GMC_oxred_C	ECOD (1.6)
A	GMC_oxred_N	e3gdpA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: GMC_oxred_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	3.30.410.40	Alpha Beta	2-Layer Sandwich	Cholesterol Oxidase	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	3.30.410.40	Alpha Beta	2-Layer Sandwich	Cholesterol Oxidase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00732	GMC oxidoreductase (GMC_oxred_N)	GMC oxidoreductase	This family of proteins bind FAD as a cofactor.	Domain
A, B	PF05199	GMC oxidoreductase (GMC_oxred_C)	GMC oxidoreductase	This domain found associated with Pfam:PF00732.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	R-oxynitrile lyase isoenzyme 1	mandelonitrile lyase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity oxidoreductase activity oxidoreductase activity, acting on CH-OH group of donors flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding mandelonitrile lyase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity oxidoreductase activity oxidoreductase activity, acting on CH-OH group of donors flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding	metabolic process cellular process nitrile metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR051871	GMC Oxidoreductase-Related Enzymes	Family
A, B	IPR000172	Glucose-methanol-choline oxidoreductase, N-terminal	Domain
A, B	IPR012132	Glucose-methanol-choline oxidoreductase	Family
A, B	IPR007867	Glucose-methanol-choline oxidoreductase, C-terminal	Domain
A, B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
B	(R)-mandelonitrile lyase M-CSA #941	Involved in cyanogenesis, the release of HCN from injured tissues. Catalyzes the stereospecific addition of HCN to a variety of aldehydes in vitro. Has no oxidase activity. The redox properties of the FAD cofactor appear to be unimportant for catalysis.	Defined by 6 residues: CYS:B-328LYS:B-361TYR:B-457HIS:B-459SER:B-496HIS:B-497 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.2.10 (PDB Primary Data) Search M-CSA Motif + EC 4.1.2.10

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.