1JRP
Crystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter capsulatus
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 | CO dehydrogenase flavoprotein C-terminal domain-like | 8037293 | 3001921 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | CO dehydrogenase ISP C-domain like | 8037287 | 3000439 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | 2Fe-2S ferredoxin-like | 8037290 | 3000113 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | FAD-binding/transporter-associated domain-like | 8037294 | 3000913 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | FAD-binding/transporter-associated domain-like | 8037294 | 3000913 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | CO dehydrogenase ISP C-domain like | 8037287 | 3000439 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | CO dehydrogenase flavoprotein C-terminal domain-like | 8037293 | 3001921 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | 2Fe-2S ferredoxin-like | 8037290 | 3000113 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | CO dehydrogenase flavoprotein C-terminal domain-like | 8037293 | 3001921 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | FAD-binding/transporter-associated domain-like | 8037294 | 3000913 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | 2Fe-2S ferredoxin-like | 8037290 | 3000113 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | CO dehydrogenase ISP C-domain like | 8037287 | 3000439 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | CO dehydrogenase ISP C-domain like | 8037287 | 3000439 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | CO dehydrogenase flavoprotein C-terminal domain-like | 8037293 | 3001921 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | 2Fe-2S ferredoxin-like | 8037290 | 3000113 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | FAD-binding/transporter-associated domain-like | 8037294 | 3000913 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Molybdenum cofactor-binding domain | 8037297 | 3000625 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | CO dehydrogenase molybdoprotein N-domain-like | 8037296 | 3000847 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | CO dehydrogenase molybdoprotein N-domain-like | 8037296 | 3000847 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Molybdenum cofactor-binding domain | 8037297 | 3000625 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | CO dehydrogenase molybdoprotein N-domain-like | 8037296 | 3000847 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Molybdenum cofactor-binding domain | 8037297 | 3000625 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | CO dehydrogenase molybdoprotein N-domain-like | 8037296 | 3000847 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | Molybdenum cofactor-binding domain | 8037297 | 3000625 | 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 | e1jrpA3 | 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 | e1jrpA4 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: Fer2 | ECOD (1.6) |
A | CO_deh_flav_C | e1jrpA2 | 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 | e1jrpA1 | 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) |
C | Fer2_2 | e1jrpC3 | 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) |
C | Fer2 | e1jrpC4 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: Fer2 | ECOD (1.6) |
C | CO_deh_flav_C | e1jrpC2 | 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) |
C | FAD_binding_5 | e1jrpC1 | 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) |
E | Fer2_2 | e1jrpE3 | 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) |
E | Fer2 | e1jrpE4 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: Fer2 | ECOD (1.6) |
E | CO_deh_flav_C | e1jrpE2 | 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) |
E | FAD_binding_5 | e1jrpE1 | 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) |
G | Fer2_2 | e1jrpG3 | 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) |
G | Fer2 | e1jrpG4 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: Fer2 | ECOD (1.6) |
G | CO_deh_flav_C | e1jrpG2 | 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) |
G | FAD_binding_5 | e1jrpG1 | 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_C2 | e1jrpB4 | 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 | Ald_Xan_dh_C | e1jrpB2 | 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) |
D | Ald_Xan_dh_C2 | e1jrpD4 | 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) |
D | Ald_Xan_dh_C | e1jrpD2 | 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) |
F | Ald_Xan_dh_C2 | e1jrpF4 | 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) |
F | Ald_Xan_dh_C | e1jrpF2 | 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) |
H | Ald_Xan_dh_C2 | e1jrpH4 | 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) |
H | Ald_Xan_dh_C | e1jrpH2 | 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 |
---|---|---|---|---|---|
PF01799 | [2Fe-2S] binding domain (Fer2_2) | [2Fe-2S] binding domain | - | Domain | |
PF03450 | CO dehydrogenase flavoprotein C-terminal domain (CO_deh_flav_C) | CO dehydrogenase flavoprotein C-terminal domain | - | Domain | |
PF00111 | 2Fe-2S iron-sulfur cluster binding domain (Fer2) | 2Fe-2S iron-sulfur cluster binding domain | - | Domain | |
PF01315 | Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain (Ald_Xan_dh_C) | Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain | - | Domain | |
PF20256 | Molybdopterin cofactor-binding domain (MoCoBD_2) | Molybdopterin cofactor-binding domain | - | Domain | |
PF02738 | Molybdopterin cofactor-binding domain (MoCoBD_1) | Molybdopterin cofactor-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 (bacterial) M-CSA #698 | Rhodobacter capsulatus xanthine dehydrogenase (RcXDH), a cytoplasmic enzyme, catalyses the hydroxylation of a wide variety of purine, pyrimidine, pterin, and aldehyde substrates. Oxidation of the substrate occurs in the molybdenum centre, and the reduced enzyme is reoxidised by the oxidant substrate, NAD+ or molecular oxygen, through FAD. The cofactors of this enzyme are located on different polypeptides. The FAD and the two different [2Fe-2S] iron-sulphur clusters are found on the XDHA subunit, while the molybdenum cofactor (Moco), with a bicyclic pterin and monocyclic pyran coordinated to it, is bound to the XDHB subunit. | EC: 1.1.1.204 (PDB Primary Data) |