2H63 | pdb_00002h63

Crystal Structure of Human Biliverdin Reductase A

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	Biliverdin reductase-like	8081406	4000092	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	GAPDH-like	8081407	3000043	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	GAPDH-like	8081407	3000043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8081407	3000043	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GAPDH-like	8081407	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)
D	Biliv-reduc_cat	e2h63D6	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)
D	GFO_IDH_MocA	e2h63D5	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)
C	Biliv-reduc_cat	e2h63C6	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)
C	GFO_IDH_MocA	e2h63C5	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)
B	Biliv-reduc_cat	e2h63B6	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)
B	GFO_IDH_MocA	e2h63B5	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)
A	Biliv-reduc_cat	e2h63A4	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	e2h63A3	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)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
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, B, C, D	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, B, C, D	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, B, C, D	Biliverdin reductase A	biliverdin reductase [NAD(P)H] activity oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity biliverdin reductase (NADPH) activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding transition metal ion binding zinc ion binding biliverdin reductase [NAD(P)H] activity oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity biliverdin reductase (NADPH) activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding biliberdin reductase (NADH) 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	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P53004	hyperbiliverdinemia Liver Cirrhosis, Experimental cholestasis acute myeloid leukemia Crohn disease lung carcinoma ovarian cancer tuberculosis Barrett esophagus esophageal adenocarcinoma malignant mesothelioma psoriasis ulcerative colitis Gaucher disease lung cancer hyperbiliverdinemia Liver Cirrhosis, Experimental cholestasis acute myeloid leukemia Crohn disease lung carcinoma ovarian cancer tuberculosis Barrett esophagus esophageal adenocarcinoma malignant mesothelioma psoriasis ulcerative colitis Gaucher disease lung cancer medulloblastoma systemic lupus erythematosus

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.