1N60 | pdb_00001n60

Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Cyanide-inactivated 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d1n60f1	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	Carbon monoxide (CO) dehydrogenase flavoprotein, C-terminal domain	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)
F	d1n60f2	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	Carbon monoxide (CO) dehydrogenase flavoprotein, N-terminal domain	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)
C	d1n60c1	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	Carbon monoxide (CO) dehydrogenase flavoprotein, C-terminal domain	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)
C	d1n60c2	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	Carbon monoxide (CO) dehydrogenase flavoprotein, N-terminal domain	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)
E	d1n60e1	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	CO dehydrogenase molybdoprotein N-domain-like	CO dehydrogenase molybdoprotein N-domain-like	Carbon monoxide (CO) dehydrogenase molybdoprotein, N-domain	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)
E	d1n60e2	Alpha and beta proteins (a+b)	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Carbon monoxide (CO) dehydrogenase molybdoprotein	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)
B	d1n60b1	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	CO dehydrogenase molybdoprotein N-domain-like	CO dehydrogenase molybdoprotein N-domain-like	Carbon monoxide (CO) dehydrogenase molybdoprotein, N-domain	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)
B	d1n60b2	Alpha and beta proteins (a+b)	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	Carbon monoxide (CO) dehydrogenase molybdoprotein	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)
D	d1n60d1	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	Carbon monoxide (CO) dehydrogenase iron-sulfur protein, C-domain	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)
D	d1n60d2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Carbone monoxide (CO) dehydrogenase iron-sulfur protein, N-domain	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)
A	d1n60a1	All alpha proteins	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	CO dehydrogenase ISP C-domain like	Carbon monoxide (CO) dehydrogenase iron-sulfur protein, C-domain	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)
A	d1n60a2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Carbone monoxide (CO) dehydrogenase iron-sulfur protein, N-domain	(Afipia carboxidovorans OM5 ) [TaxId: 504832 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	CO dehydrogenase flavoprotein C-terminal domain-like	8043532	3001921	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	FAD-binding/transporter-associated domain-like	8043534	3000913	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CO dehydrogenase flavoprotein C-terminal domain-like	8043532	3001921	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FAD-binding/transporter-associated domain-like	8043534	3000913	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	CO dehydrogenase molybdoprotein N-domain-like	8043530	3000847	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Molybdenum cofactor-binding domain	8043531	3000625	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CO dehydrogenase molybdoprotein N-domain-like	8043530	3000847	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Molybdenum cofactor-binding domain	8043531	3000625	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8043528	3000113	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CO dehydrogenase ISP C-domain like	8043526	3000439	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8043528	3000113	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CO dehydrogenase ISP C-domain like	8043526	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)
F	YceM-like_C	e1n60F1	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.2)
F	LRR_6,LRR_RI_capping	e1n60F2	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: LRR_6,LRR_RI_capping	ECOD (v294.2)
C	YceM-like_C	e1n60C1	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.2)
C	LRR_6,LRR_RI_capping	e1n60C2	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: LRR_6,LRR_RI_capping	ECOD (v294.2)
E	Biotin_carb_C	e1n60E2	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.2)
E	ThiF	e1n60E1	A: beta barrels	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: ThiF	ECOD (v294.2)
B	Biotin_carb_C	e1n60B2	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.2)
B	ThiF	e1n60B3	A: beta barrels	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: ThiF	ECOD (v294.2)
D	PAP2	e1n60D1	A: beta barrels	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: PAP2	ECOD (v294.2)
D	S4	e1n60D2	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.2)
A	PAP2	e1n60A1	A: beta barrels	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: PAP2	ECOD (v294.2)
A	S4	e1n60A2	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
F	3.30.390.50	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
F	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	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	3.30.390.50	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	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)
E	3.90.1170.50	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
E	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)
D	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
D	1.10.150.120	Mainly Alpha	Orthogonal Bundle	DNA polymerase	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Source
C, F	PF00941	FAD binding domain in molybdopterin dehydrogenase (FAD_binding_5)	FAD binding domain in molybdopterin dehydrogenase	Domain
C, F	PF03450	CO dehydrogenase flavoprotein C-terminal domain (CO_deh_flav_C)	CO dehydrogenase flavoprotein C-terminal domain	Domain
B, E	PF01315	Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain (Ald_Xan_dh_C)	Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain	Domain
B, E	PF20256	Molybdopterin cofactor-binding domain (MoCoBD_2)	Molybdopterin cofactor-binding domain	Domain
B, E	PF02738	Molybdopterin cofactor-binding domain (MoCoBD_1)	Molybdopterin cofactor-binding domain	Domain
A, D	PF01799	[2Fe-2S] binding domain (Fer2_2)	[2Fe-2S] binding domain	Domain
A, D	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
C, F	Carbon monoxide dehydrogenase medium chain	oxidoreductase activity, acting on the aldehyde or oxo group of donors, cytochrome as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity carbon-monoxide oxygenase activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding	-	-
B, E	Carbon monoxide dehydrogenase large chain	anaerobic carbon-monoxide dehydrogenase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding molybdenum ion binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, cytochrome as acceptor anaerobic carbon-monoxide dehydrogenase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding molybdenum ion binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, cytochrome as acceptor carbon-monoxide oxygenase activity iron ion binding	-	-
A, D	Carbon monoxide dehydrogenase small chain	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, cytochrome as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity carbon-monoxide oxygenase activity cation binding ion binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR016167	FAD-binding, type PCMH, subdomain 1	Homologous Superfamily
C, F	IPR036683	CO dehydrogenase flavoprotein, C-terminal domain superfamily	Homologous Superfamily
C, F	IPR051312	Diverse Substrate Oxidoreductases	Family
C, F	IPR036318	FAD-binding, type PCMH-like superfamily	Homologous Superfamily
C, F	IPR016169	FAD-binding, type PCMH, subdomain 2	Homologous Superfamily
C, F	IPR016166	FAD-binding domain, PCMH-type	Domain
C, F	IPR005107	CO dehydrogenase flavoprotein, C-terminal	Domain
C, F	IPR002346	Molybdopterin dehydrogenase, FAD-binding	Domain
B, E	IPR046867	Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain	Domain
B, E	IPR000674	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead	Domain
B, E	IPR012780	Carbon-monoxide dehydrogenase, large subunit	Family
B, E	IPR016208	Aldehyde oxidase/xanthine dehydrogenase-like	Family
B, E	IPR036856	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily	Homologous Superfamily
B, E	IPR037165	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily	Homologous Superfamily
B, E	IPR008274	Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain	Domain
A, D	IPR002888	[2Fe-2S]-binding	Domain
A, D	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
A, D	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
A, D	IPR036884	[2Fe-2S]-binding domain superfamily	Homologous Superfamily
A, D	IPR051452	Diverse Oxidoreductases	Family
A, D	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily

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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.