2W3S | pdb_00002w3s

Crystal Structure of Xanthine Dehydrogenase (desulfo form) from Rhodobacter capsulatus in Complex with Xanthine

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d2w3sh1	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	d2w3sh2	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	d2w3sf1	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	d2w3sf2	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	d2w3sd1	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	d2w3sd2	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)
B	d2w3sb1	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	d2w3sb2	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)
G	d2w3sg2	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
G	d2w3sg1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
G	d2w3sg4	Alpha and beta proteins (a+b)	CO dehydrogenase flavoprotein C-domain-like	CO dehydrogenase flavoprotein C-terminal domain-like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
G	d2w3sg3	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
E	d2w3se2	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
E	d2w3se1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
E	d2w3se4	Alpha and beta proteins (a+b)	CO dehydrogenase flavoprotein C-domain-like	CO dehydrogenase flavoprotein C-terminal domain-like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
E	d2w3se3	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
C	d2w3sc2	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
C	d2w3sc1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
C	d2w3sc4	Alpha and beta proteins (a+b)	CO dehydrogenase flavoprotein C-domain-like	CO dehydrogenase flavoprotein C-terminal domain-like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
C	d2w3sc3	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
A	d2w3sa2	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
A	d2w3sa1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
A	d2w3sa4	Alpha and beta proteins (a+b)	CO dehydrogenase flavoprotein C-domain-like	CO dehydrogenase flavoprotein C-terminal domain-like	automated matches	automated matches	(Rhodobacter capsulatus ) [TaxId: 1061 ],	SCOPe (2.08)
A	d2w3sa3	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	automated matches	automated matches	(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)
H	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)
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)
D	SCOP2B Superfamily	Molybdenum cofactor-binding domain	8037297	3000625	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CO dehydrogenase molybdoprotein N-domain-like	8037296	3000847	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)
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	FAD-binding/transporter-associated domain-like	8037294	3000913	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8037290	3000113	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8037290	3000113	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	FAD-binding/transporter-associated domain-like	8037294	3000913	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	CO dehydrogenase ISP C-domain like	8037287	3000439	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	CO dehydrogenase flavoprotein C-terminal domain-like	8037293	3001921	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	FAD-binding/transporter-associated domain-like	8037294	3000913	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8037290	3000113	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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	Fe_hyd_lg_C	e2w3sH3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fe_hyd_lg_C	ECOD (v294.1)
H	Adaptin_N, Cnd1	e2w3sH2	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Adaptin_N, Cnd1	ECOD (v294.1)
F	Fe_hyd_lg_C	e2w3sF3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fe_hyd_lg_C	ECOD (v294.1)
F	Adaptin_N, Cnd1	e2w3sF2	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Adaptin_N, Cnd1	ECOD (v294.1)
D	Fe_hyd_lg_C	e2w3sD3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fe_hyd_lg_C	ECOD (v294.1)
D	Adaptin_N, Cnd1	e2w3sD2	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Adaptin_N, Cnd1	ECOD (v294.1)
B	Fe_hyd_lg_C	e2w3sB3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fe_hyd_lg_C	ECOD (v294.1)
B	Adaptin_N, Cnd1	e2w3sB2	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Adaptin_N, Cnd1	ECOD (v294.1)
G		e2w3sG1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)
E		e2w3sE1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)
C		e2w3sC1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)
A		e2w3sA1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)
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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	XANTHINE DEHYDROGENASE	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	-	-
A, C, E, G	XANTHINE DEHYDROGENASE	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	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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