1N5X | pdb_00001n5x

Xanthine Dehydrogenase from Bovine Milk with Inhibitor TEI-6720 Bound

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	d1n5xa1	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	Xanthine oxidase, domain 2	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d1n5xa2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Xanthine oxidase, N-terminal domain	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d1n5xa3	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	CO dehydrogenase molybdoprotein N-domain-like	CO dehydrogenase molybdoprotein N-domain-like	Xanthine oxidase, domain 5 (?)	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d1n5xa4	Alpha and beta proteins (a+b)	CO dehydrogenase flavoprotein C-domain-like	CO dehydrogenase flavoprotein C-terminal domain-like	CO dehydrogenase flavoprotein C-terminal domain-like	Xanthine oxidase, domain 4 (?)	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d1n5xa5	Alpha and beta proteins (a+b)	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Xanthine oxidase, C-terminal domain	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d1n5xa6	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	CO dehydrogenase flavoprotein N-terminal domain-like	Xanthine oxidase, domain 3 (?)	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B	d1n5xb1	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	Xanthine oxidase, domain 2	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B	d1n5xb2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Xanthine oxidase, N-terminal domain	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B	d1n5xb3	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	CO dehydrogenase molybdoprotein N-domain-like	CO dehydrogenase molybdoprotein N-domain-like	Xanthine oxidase, domain 5 (?)	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B	d1n5xb4	Alpha and beta proteins (a+b)	CO dehydrogenase flavoprotein C-domain-like	CO dehydrogenase flavoprotein C-terminal domain-like	CO dehydrogenase flavoprotein C-terminal domain-like	Xanthine oxidase, domain 4 (?)	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B	d1n5xb5	Alpha and beta proteins (a+b)	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Xanthine oxidase, C-terminal domain	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B	d1n5xb6	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	CO dehydrogenase flavoprotein N-terminal domain-like	Xanthine oxidase, domain 3 (?)	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	CO dehydrogenase molybdoprotein N-domain-like	8043059	3000847	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FAD-binding/transporter-associated domain-like	8043065	3000913	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Molybdenum cofactor-binding domain	8043062	3000625	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CO dehydrogenase ISP C-domain like	8043057	3000439	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8043058	3000113	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CO dehydrogenase flavoprotein C-terminal domain-like	8043061	3001921	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CO dehydrogenase molybdoprotein N-domain-like	8043059	3000847	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CO dehydrogenase ISP C-domain like	8043057	3000439	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CO dehydrogenase flavoprotein C-terminal domain-like	8043061	3001921	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Molybdenum cofactor-binding domain	8043062	3000625	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8043058	3000113	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FAD-binding/transporter-associated domain-like	8043065	3000913	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	PAP2	e1n5xA1	A: beta barrels	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: PAP2	ECOD (v294.2)
A	S4	e1n5xA3	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.2)
A	YceM-like_C	e1n5xA4	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.2)
A	LRR_6,LRR_RI_capping	e1n5xA5	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: LRR_6,LRR_RI_capping	ECOD (v294.2)
A	Biotin_carb_C	e1n5xA6	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.2)
A	ThiF	e1n5xA7	A: beta barrels	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: ThiF	ECOD (v294.2)
B	PAP2	e1n5xB1	A: beta barrels	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: PAP2	ECOD (v294.2)
B	S4	e1n5xB3	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.2)
B	YceM-like_C	e1n5xB4	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.2)
B	LRR_6,LRR_RI_capping	e1n5xB5	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: LRR_6,LRR_RI_capping	ECOD (v294.2)
B	Biotin_carb_C	e1n5xB6	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.2)
B	ThiF	e1n5xB7	A: beta barrels	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: ThiF	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
A	1.10.150.120	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
A	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
A	3.30.390.50	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
A	3.30.365.10	Alpha Beta	2-Layer Sandwich	Aldehyde Oxidoreductase	domain 4	CATH (4.3.0)
A	3.90.1170.50	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
B	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
B	1.10.150.120	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
B	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
B	3.30.390.50	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
B	3.30.365.10	Alpha Beta	2-Layer Sandwich	Aldehyde Oxidoreductase	domain 4	CATH (4.3.0)
B	3.90.1170.50	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Source
A, B	PF00941	FAD binding domain in molybdopterin dehydrogenase (FAD_binding_5)	FAD binding domain in molybdopterin dehydrogenase	Domain
A, B	PF01315	Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain (Ald_Xan_dh_C)	Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain	Domain
A, B	PF01799	[2Fe-2S] binding domain (Fer2_2)	[2Fe-2S] binding domain	Domain
A, B	PF20256	Molybdopterin cofactor-binding domain (MoCoBD_2)	Molybdopterin cofactor-binding domain	Domain
A, B	PF03450	CO dehydrogenase flavoprotein C-terminal domain (CO_deh_flav_C)	CO dehydrogenase flavoprotein C-terminal domain	Domain
A, B	PF02738	Molybdopterin cofactor-binding domain (MoCoBD_1)	Molybdopterin cofactor-binding domain	Domain
A, B	PF00111	2Fe-2S iron-sulfur cluster binding domain (Fer2)	2Fe-2S iron-sulfur cluster binding domain	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Xanthine Dehydrogenase	FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor xanthine dehydrogenase activity catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor xanthine dehydrogenase activity catalytic activity identical protein binding protein binding protein homodimerization activity protein dimerization activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding metal cluster binding cation binding transition metal ion binding iron ion binding metal ion binding molybdenum ion binding molybdopterin cofactor binding oxidoreductase activity, acting on CH or CH2 groups, oxygen as acceptor xanthine oxidase activity	catabolic process purine nucleobase metabolic process primary metabolic process purine-containing compound catabolic process xanthine metabolic process purine nucleobase catabolic process purine-containing compound metabolic process xanthine catabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process nucleobase catabolic process nucleobase metabolic process small molecule metabolic process metabolic process catabolic process purine nucleobase metabolic process primary metabolic process purine-containing compound catabolic process xanthine metabolic process purine nucleobase catabolic process purine-containing compound metabolic process xanthine catabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process nucleobase catabolic process nucleobase metabolic process small molecule metabolic process metabolic process cellular process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle peroxisome microbody cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex xanthine dehydrogenase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016167	FAD-binding, type PCMH, subdomain 1	Homologous Superfamily
A, B	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
A, B	IPR006058	2Fe-2S ferredoxin, iron-sulphur binding site	Binding Site
A, B	IPR046867	Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain	Domain
A, B	IPR002888	[2Fe-2S]-binding	Domain
A, B	IPR036318	FAD-binding, type PCMH-like superfamily	Homologous Superfamily
A, B	IPR016208	Aldehyde oxidase/xanthine dehydrogenase-like	Family
A, B	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
A, B	IPR036683	CO dehydrogenase flavoprotein, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
A, B	IPR000674	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead	Domain
A, B	IPR022407	Oxidoreductase, molybdopterin binding site	Binding Site
A, B	IPR036856	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily	Homologous Superfamily
A, B	IPR037165	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily	Homologous Superfamily
A, B	IPR016166	FAD-binding domain, PCMH-type	Domain
A, B	IPR002346	Molybdopterin dehydrogenase, FAD-binding	Domain
A, B	IPR014307	Xanthine dehydrogenase, small subunit	Domain
A, B	IPR016169	FAD-binding, type PCMH, subdomain 2	Homologous Superfamily
A, B	IPR036884	[2Fe-2S]-binding domain superfamily	Homologous Superfamily
A, B	IPR008274	Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain	Domain
A, B	IPR005107	CO dehydrogenase flavoprotein, C-terminal	Domain

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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.