1V97
Crystal Structure of Bovine Milk Xanthine Dehydrogenase FYX-051 bound form
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
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
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00941 | FAD binding domain in molybdopterin dehydrogenase (FAD_binding_5) | FAD binding domain in molybdopterin dehydrogenase | - | Family | |
PF01315 | Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain (Ald_Xan_dh_C) | Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain | - | Domain | |
PF01799 | [2Fe-2S] binding domain (Fer2_2) | [2Fe-2S] binding domain | - | Domain | |
PF20256 | Molybdopterin cofactor-binding domain (MoCoBD_2) | Molybdopterin cofactor-binding domain | - | Domain | |
PF03450 | CO dehydrogenase flavoprotein C-terminal domain (CO_deh_flav_C) | CO dehydrogenase flavoprotein C-terminal domain | - | Domain | |
PF02738 | Molybdopterin cofactor-binding domain (MoCoBD_1) | Molybdopterin cofactor-binding domain | - | Domain | |
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
InterPro: Protein Family Classification InterPro Database Homepage
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
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. | EC: 1.1.1.204 (PDB Primary Data) EC: 1.17.1.4 (UniProt) EC: 1.17.3.2 (UniProt) |