1JRP | pdb_00001jrp

Crystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter capsulatus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d1jrpa1	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	Xanthine dehydrogenase chain A, domain 2	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
A	d1jrpa2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Xanthine dehydrogenase chain A, N-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
A	d1jrpa3	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 dehydrogenase chain A, domain 4	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
A	d1jrpa4	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 dehydrogenase chain A, domain 3	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
C	d1jrpc1	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	Xanthine dehydrogenase chain A, domain 2	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
C	d1jrpc2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Xanthine dehydrogenase chain A, N-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
C	d1jrpc3	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 dehydrogenase chain A, domain 4	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
C	d1jrpc4	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 dehydrogenase chain A, domain 3	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
G	d1jrpg1	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	Xanthine dehydrogenase chain A, domain 2	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
G	d1jrpg2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Xanthine dehydrogenase chain A, N-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
G	d1jrpg3	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 dehydrogenase chain A, domain 4	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
G	d1jrpg4	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 dehydrogenase chain A, domain 3	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
E	d1jrpe1	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	Xanthine dehydrogenase chain A, domain 2	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
E	d1jrpe2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Xanthine dehydrogenase chain A, N-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
E	d1jrpe3	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 dehydrogenase chain A, domain 4	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
E	d1jrpe4	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 dehydrogenase chain A, domain 3	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
B	d1jrpb1	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	CO dehydrogenase molybdoprotein N-domain-like	CO dehydrogenase molybdoprotein N-domain-like	Xanthine dehydrogenase chain B, N-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
B	d1jrpb2	Alpha and beta proteins (a+b)	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Xanthine dehydrogenase chain B, C-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
D	d1jrpd1	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	CO dehydrogenase molybdoprotein N-domain-like	CO dehydrogenase molybdoprotein N-domain-like	Xanthine dehydrogenase chain B, N-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
D	d1jrpd2	Alpha and beta proteins (a+b)	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Xanthine dehydrogenase chain B, C-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
H	d1jrph1	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	CO dehydrogenase molybdoprotein N-domain-like	CO dehydrogenase molybdoprotein N-domain-like	Xanthine dehydrogenase chain B, N-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
H	d1jrph2	Alpha and beta proteins (a+b)	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Xanthine dehydrogenase chain B, C-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
F	d1jrpf1	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	CO dehydrogenase molybdoprotein N-domain-like	CO dehydrogenase molybdoprotein N-domain-like	Xanthine dehydrogenase chain B, N-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
F	d1jrpf2	Alpha and beta proteins (a+b)	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Xanthine dehydrogenase chain B, C-terminal domain	(Rhodobacter capsulatus ) [TaxId: 1061 ],	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 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)
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)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	e1jrpA1	A: amino-terminal domain of OmpATb	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T:	F:	ECOD (20:10:01)
C	e1jrpC1	A: amino-terminal domain of OmpATb	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T:	F:	ECOD (20:10:01)
G	e1jrpG1	A: amino-terminal domain of OmpATb	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T:	F:	ECOD (20:10:01)
E	e1jrpE1	A: amino-terminal domain of OmpATb	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T:	F:	ECOD (20:10:01)
B	e1jrpB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
B	e1jrpB3	A: HTH	X: HTH	H: winged helix domain	T: Glycogen_syn	F:	ECOD (20:10:01)
D	e1jrpD2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
D	e1jrpD3	A: HTH	X: HTH	H: winged helix domain	T: Glycogen_syn	F:	ECOD (20:10:01)
H	e1jrpH2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
H	e1jrpH3	A: HTH	X: HTH	H: winged helix domain	T: Glycogen_syn	F:	ECOD (20:10:01)
F	e1jrpF2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
F	e1jrpF3	A: HTH	X: HTH	H: winged helix domain	T: Glycogen_syn	F:	ECOD (20:10:01)

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	3.30.390.50	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
C	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
C	1.10.150.120	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
C	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
C	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
C	3.30.390.50	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
G	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
G	1.10.150.120	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
G	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
G	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
G	3.30.390.50	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
E	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
E	1.10.150.120	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
E	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
E	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
E	3.30.390.50	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
B	3.90.1170.50	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
B	3.30.365.10	Alpha Beta	2-Layer Sandwich	Aldehyde Oxidoreductase	domain 4	CATH (4.3.0)
D	3.90.1170.50	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
D	3.30.365.10	Alpha Beta	2-Layer Sandwich	Aldehyde Oxidoreductase	domain 4	CATH (4.3.0)
H	3.90.1170.50	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
H	3.30.365.10	Alpha Beta	2-Layer Sandwich	Aldehyde Oxidoreductase	domain 4	CATH (4.3.0)
F	3.90.1170.50	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
F	3.30.365.10	Alpha Beta	2-Layer Sandwich	Aldehyde Oxidoreductase	domain 4	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	xanthine dehydrogenase, chain A	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding cation binding transition metal ion binding iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding cation binding transition metal ion binding iron ion binding metal ion 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	-	-
B, D, F, H	xanthine dehydrogenase, chain B	oxidoreductase activity catalytic activity cation binding transition metal ion binding molybdenum ion binding ion binding binding metal ion binding small molecule binding iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding metal cluster binding iron ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR016167	FAD-binding, type PCMH, subdomain 1	Homologous Superfamily
A, C, E, G	IPR036683	CO dehydrogenase flavoprotein, C-terminal domain superfamily	Homologous Superfamily
A, C, E, G	IPR012175	Xanthine dehydrogenase, small subunit, bacteria	Family
A, C, E, G	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
A, C, E, G	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
A, C, E, G	IPR006058	2Fe-2S ferredoxin, iron-sulphur binding site	Binding Site
A, C, E, G	IPR016166	FAD-binding domain, PCMH-type	Domain
A, C, E, G	IPR002346	Molybdopterin dehydrogenase, FAD-binding	Domain
A, C, E, G	IPR014307	Xanthine dehydrogenase, small subunit	Domain
A, C, E, G	IPR002888	[2Fe-2S]-binding	Domain
A, C, E, G	IPR036318	FAD-binding, type PCMH-like superfamily	Homologous Superfamily
A, C, E, G	IPR016169	FAD-binding, type PCMH, subdomain 2	Homologous Superfamily
A, C, E, G	IPR036884	[2Fe-2S]-binding domain superfamily	Homologous Superfamily
A, C, E, G	IPR016208	Aldehyde oxidase/xanthine dehydrogenase-like	Family
A, C, E, G	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
A, C, E, G	IPR005107	CO dehydrogenase flavoprotein, C-terminal	Domain
B, D, F, H	IPR046867	Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain	Domain
B, D, F, H	IPR000674	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead	Domain
B, D, F, H	IPR014309	Xanthine dehydrogenase, molybdopterin binding subunit	Domain
B, D, F, H	IPR016208	Aldehyde oxidase/xanthine dehydrogenase-like	Family
B, D, F, H	IPR036856	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily	Homologous Superfamily
B, D, F, H	IPR037165	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily	Homologous Superfamily
B, D, F, H	IPR008274	Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
B	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.	Defined by 2 residues: ARG:B-310GLU:B-730 \| 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

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.

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 1JRP | pdb_00001jrp