5JAB

Structure of the biliverdin reductase Rv2074 from Mycobacterium tuberculosis in complex with F420

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	d5jaba_	All beta proteins	Split barrel-like	FMN-binding split barrel	PNP-oxidase like	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
B	d5jabb_	All beta proteins	Split barrel-like	FMN-binding split barrel	PNP-oxidase like	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
C	d5jabc_	All beta proteins	Split barrel-like	FMN-binding split barrel	PNP-oxidase like	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
D	d5jabd_	All beta proteins	Split barrel-like	FMN-binding split barrel	PNP-oxidase like	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FMN-binding split barrel	8037328	3000856	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FMN-binding split barrel	8037328	3000856	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FMN-binding split barrel	8037328	3000856	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	FMN-binding split barrel	8037328	3000856	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	Putative_PNPOx	e5jabA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Putative_PNPOx	ECOD (1.6)
B	Putative_PNPOx	e5jabB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Putative_PNPOx	ECOD (1.6)
C	Putative_PNPOx	e5jabC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Putative_PNPOx	ECOD (1.6)
D	Putative_PNPOx	e5jabD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Putative_PNPOx	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
B	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
C	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
D	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01243	Pyridoxamine 5'-phosphate oxidase (Putative_PNPOx)	Pyridoxamine 5'-phosphate oxidase	Family of domains with putative PNPOx function. Family members were predicted to encode pyridoxamine 5'-phosphate oxidase, based on sequence similarity. However, there is no experimental data to validate the predicted activity and purified proteins, ...	Family of domains with putative PNPOx function. Family members were predicted to encode pyridoxamine 5'-phosphate oxidase, based on sequence similarity. However, there is no experimental data to validate the predicted activity and purified proteins, such as Swiss:Q06199 and its paralogs, do not possess this activity, nor do they bind to flavin mononucleotide (FMN). To date, the only time functional oxidase activity has been experimentally demonstrated is when the sequences contain both Pfam:PF01243 and Pfam:PF10590. Moreover, some of the family members that contain both domains have been shown to be involved in phenazine biosynthesis. While some molecular function has been experimentally validated for the proteins containing both domains, the role performed by each domain on its own is unknown [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 Rv2074	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity organic acid binding ion binding organic cyclic compound binding anion binding coenzyme F420 binding carboxylic acid binding heterocyclic compound binding carbohydrate derivative binding small molecule binding identical protein binding protein binding binding protein homodimerization activity protein dimerization activity organic acid binding ion binding organic cyclic compound binding anion binding coenzyme F420 binding carboxylic acid binding heterocyclic compound binding carbohydrate derivative binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity	-	cell surface cellular anatomical entity cell periphery external encapsulating structure cell wall peptidoglycan-based cell wall extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR019920	F420-binding domain, putative	Domain
A, B, C, D	IPR012349	FMN-binding split barrel	Homologous Superfamily
A, B, C, D	IPR011576	Pyridoxamine 5'-phosphate oxidase, putative	Domain
A, B, C, D	IPR052019	F420H(2)-dependent biliverdin reductase/Heme oxygenase	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.