1LC3

Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex

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	d1lc3a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Biliverdin reductase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1lc3a2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Biliverdin reductase	Biliverdin reductase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	GAPDH-like	8000942	3000043	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	Biliv-reduc_cat	e1lc3A1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: Biliv-reduc_cat	ECOD (1.6)
A	GFO_IDH_MocA	e1lc3A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GFO_IDH_MocA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01408	Oxidoreductase family, NAD-binding Rossmann fold (GFO_IDH_MocA)	Oxidoreductase family, NAD-binding Rossmann fold	This entry represents the N-terminal domain of a group of enzymes that utilise NADP or NAD, known as the GFO/IDH/MOCA family, which includes enzymes that catalyse different chemical reactions such as oxidation and reduction of carbohydrates, oxidatio ...	This entry represents the N-terminal domain of a group of enzymes that utilise NADP or NAD, known as the GFO/IDH/MOCA family, which includes enzymes that catalyse different chemical reactions such as oxidation and reduction of carbohydrates, oxidation of trans-dihydrodiols, reduction of biliverdin and hydrolysation of glycosidic bonds. This domain adopts a a typical Rossmann fold.	Domain
A	PF09166	Biliverdin reductase, catalytic (Biliv-reduc_cat)	Biliverdin reductase, catalytic	Members of this family adopt a structure consisting of four alpha helices and six beta sheets, in an alpha-beta-alpha-alpha-alpha-beta-beta-beta-beta-beta arrangement. They contain a catalytic active site, capable of reducing the gamma-methene bridge ...	Members of this family adopt a structure consisting of four alpha helices and six beta sheets, in an alpha-beta-alpha-alpha-alpha-beta-beta-beta-beta-beta arrangement. They contain a catalytic active site, capable of reducing the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Biliverdin Reductase A	oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor biliverdin reductase [NAD(P)+] activity biliverdin reductase (NADP+) activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor biliverdin reductase [NAD(P)+] activity biliverdin reductase (NADP+) activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding biliberdin reductase (NAD+) activity	pigment catabolic process pigment metabolic process heme metabolic process catabolic process tetrapyrrole metabolic process heme catabolic process porphyrin-containing compound catabolic process metabolic process cellular process porphyrin-containing compound metabolic process tetrapyrrole catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017094	Biliverdin reductase A	Family
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR015249	Biliverdin reductase, catalytic	Domain
A	IPR051450	Gfo/Idh/MocA Oxidoreductases	Family
A	IPR000683	Gfo/Idh/MocA-like oxidoreductase, 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.