1V97

Crystal Structure of Bovine Milk Xanthine Dehydrogenase FYX-051 bound form

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1v97a1	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	d1v97a2	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	d1v97a3	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	d1v97a4	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	d1v97a5	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	d1v97a6	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	d1v97b1	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	d1v97b2	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	d1v97b3	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	d1v97b4	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	d1v97b5	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	d1v97b6	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	FAD-binding/transporter-associated domain-like	8043065	3000913	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 molybdoprotein N-domain-like	8043059	3000847	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CO dehydrogenase flavoprotein C-terminal domain-like	8043061	3001921	SCOP2B (2022-06-29)
A	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	CO dehydrogenase molybdoprotein N-domain-like	8043059	3000847	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CO dehydrogenase flavoprotein C-terminal domain-like	8043061	3001921	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CO dehydrogenase ISP C-domain like	8043057	3000439	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Molybdenum cofactor-binding domain	8043062	3000625	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	Fer2_2	e1v97A1	A: alpha bundles	X: CO dehydrogenase ISP C-domain like (From Topology)	H: CO dehydrogenase ISP C-domain like (From Topology)	T: CO dehydrogenase ISP C-domain like	F: Fer2_2	ECOD (1.6)
A	Fer2	e1v97A3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
A	Ald_Xan_dh_C2	e1v97A7	A: a+b two layers	X: MocoBD/DmpA-related (From Homology)	H: MocoBD/DmpA-related	T: Molybdenum cofactor-binding domain	F: Ald_Xan_dh_C2	ECOD (1.6)
A	CO_deh_flav_C	e1v97A4	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: SufE/NifU (From Topology)	T: SufE/NifU	F: CO_deh_flav_C	ECOD (1.6)
A	FAD_binding_5	e1v97A5	A: a+b complex topology	X: FAD-binding domain-like	H: FAD-binding domain (From Topology)	T: FAD-binding domain	F: FAD_binding_5	ECOD (1.6)
A	Ald_Xan_dh_C	e1v97A6	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Ald_Xan_dh_C	ECOD (1.6)
B	Fer2_2	e1v97B1	A: alpha bundles	X: CO dehydrogenase ISP C-domain like (From Topology)	H: CO dehydrogenase ISP C-domain like (From Topology)	T: CO dehydrogenase ISP C-domain like	F: Fer2_2	ECOD (1.6)
B	Fer2	e1v97B3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
B	Ald_Xan_dh_C2	e1v97B7	A: a+b two layers	X: MocoBD/DmpA-related (From Homology)	H: MocoBD/DmpA-related	T: Molybdenum cofactor-binding domain	F: Ald_Xan_dh_C2	ECOD (1.6)
B	CO_deh_flav_C	e1v97B4	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: SufE/NifU (From Topology)	T: SufE/NifU	F: CO_deh_flav_C	ECOD (1.6)
B	FAD_binding_5	e1v97B5	A: a+b complex topology	X: FAD-binding domain-like	H: FAD-binding domain (From Topology)	T: FAD-binding domain	F: FAD_binding_5	ECOD (1.6)
B	Ald_Xan_dh_C	e1v97B6	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Ald_Xan_dh_C	ECOD (1.6)

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	Comments	Source
A, B	PF00941	FAD binding domain in molybdopterin dehydrogenase (FAD_binding_5)	FAD binding domain in molybdopterin dehydrogenase	-	Family
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 organic cyclic compound 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 FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound 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	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle peroxisome microbody cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex xanthine dehydrogenase complex extracellular region membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle peroxisome microbody cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex xanthine dehydrogenase complex extracellular region extracellular space

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

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

Chains	Enzyme Name	Description	Catalytic Residues
A	xanthine dehydrogenase (mammalian) M-CSA #139	Mammalian xanthine oxidoreductase catalyses the hydroxylation of hypoxanthine and xanthine, the last two stages in the biosynthesis pathway of urate. The enzyme is first formed as xanthine dehydrogenase (XDH), and exists mostly in this form within the cell but it can be readily converted to the oxidase form xanthine oxidase (XO) by oxidation of sulfhydryl residues or by proteolysis. The active form of the enzyme is a homodimer of a three chain subunits, where both units contain one molybdenum centre, one flavin (FAD) centre and two Fe-S clusters. The oxidation of xanthine to uric acid takes place at the molybdenum centre and results in a two electron reduction of the metal from Mo(VI) to Mo(IV). The enzyme is subsequently reoxidised by molecular oxygen in a reaction that occurs at the FAD cofactor. Xanthine dehydrogenase (EC 1.17.1.4) and xanthine oxidase (EC 1.17.3.2 - M-CSA ID:987) are two variants of the same gene product. The former prefers NAD+ as the oxidising substrate whereas the latter uses dioxygen exclusively.	Defined by 3 residues: GLU:A-802ARG:A-880GLU:A-1261 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.1.1.204 (PDB Primary Data) Search M-CSA Motif + EC 1.1.1.204 EC: 1.17.1.4 (UniProt) Search M-CSA Motif + EC 1.17.1.4 EC: 1.17.3.2 (UniProt) Search M-CSA Motif + EC 1.17.3.2