6OND | pdb_00006ond

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase produced without CooC, reduced

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Prismane_2nd	e6ondD3	A: alpha bundles	X: Helical bundle domain in prismane-like proteins (From Topology)	H: Helical bundle domain in prismane-like proteins (From Topology)	T: Helical bundle domain in prismane-like proteins	F: Prismane_2nd	ECOD (1.6)
D	Prismane_4th	e6ondD4	A: a/b three-layered sandwiches	X: Rossmann-like domain in prismane-like proteins (From Topology)	H: Rossmann-like domain in prismane-like proteins (From Topology)	T: Rossmann-like domain in prismane-like proteins	F: Prismane_4th	ECOD (1.6)
D	Prismane_3rd	e6ondD2	A: a/b three-layered sandwiches	X: Rossmann-like domain in prismane-like proteins (From Topology)	H: Rossmann-like domain in prismane-like proteins (From Topology)	T: Rossmann-like domain in prismane-like proteins	F: Prismane_3rd	ECOD (1.6)
D	CODH	e6ondD1	A: few secondary structure elements	X: Fe-binding domain in prismane-like proteins (From Topology)	H: Fe-binding domain in prismane-like proteins (From Topology)	T: Fe-binding domain in prismane-like proteins	F: CODH	ECOD (1.6)
C	Prismane_2nd	e6ondC1	A: alpha bundles	X: Helical bundle domain in prismane-like proteins (From Topology)	H: Helical bundle domain in prismane-like proteins (From Topology)	T: Helical bundle domain in prismane-like proteins	F: Prismane_2nd	ECOD (1.6)
C	Prismane_4th	e6ondC4	A: a/b three-layered sandwiches	X: Rossmann-like domain in prismane-like proteins (From Topology)	H: Rossmann-like domain in prismane-like proteins (From Topology)	T: Rossmann-like domain in prismane-like proteins	F: Prismane_4th	ECOD (1.6)
C	Prismane_3rd	e6ondC3	A: a/b three-layered sandwiches	X: Rossmann-like domain in prismane-like proteins (From Topology)	H: Rossmann-like domain in prismane-like proteins (From Topology)	T: Rossmann-like domain in prismane-like proteins	F: Prismane_3rd	ECOD (1.6)
C	CODH	e6ondC2	A: few secondary structure elements	X: Fe-binding domain in prismane-like proteins (From Topology)	H: Fe-binding domain in prismane-like proteins (From Topology)	T: Fe-binding domain in prismane-like proteins	F: CODH	ECOD (1.6)
B	Prismane_2nd	e6ondB3	A: alpha bundles	X: Helical bundle domain in prismane-like proteins (From Topology)	H: Helical bundle domain in prismane-like proteins (From Topology)	T: Helical bundle domain in prismane-like proteins	F: Prismane_2nd	ECOD (1.6)
B	Prismane_4th	e6ondB2	A: a/b three-layered sandwiches	X: Rossmann-like domain in prismane-like proteins (From Topology)	H: Rossmann-like domain in prismane-like proteins (From Topology)	T: Rossmann-like domain in prismane-like proteins	F: Prismane_4th	ECOD (1.6)
B	Prismane_3rd	e6ondB4	A: a/b three-layered sandwiches	X: Rossmann-like domain in prismane-like proteins (From Topology)	H: Rossmann-like domain in prismane-like proteins (From Topology)	T: Rossmann-like domain in prismane-like proteins	F: Prismane_3rd	ECOD (1.6)
B	CODH	e6ondB1	A: few secondary structure elements	X: Fe-binding domain in prismane-like proteins (From Topology)	H: Fe-binding domain in prismane-like proteins (From Topology)	T: Fe-binding domain in prismane-like proteins	F: CODH	ECOD (1.6)
A	Prismane_2nd	e6ondA1	A: alpha bundles	X: Helical bundle domain in prismane-like proteins (From Topology)	H: Helical bundle domain in prismane-like proteins (From Topology)	T: Helical bundle domain in prismane-like proteins	F: Prismane_2nd	ECOD (1.6)
A	Prismane_4th	e6ondA2	A: a/b three-layered sandwiches	X: Rossmann-like domain in prismane-like proteins (From Topology)	H: Rossmann-like domain in prismane-like proteins (From Topology)	T: Rossmann-like domain in prismane-like proteins	F: Prismane_4th	ECOD (1.6)
A	Prismane_3rd	e6ondA4	A: a/b three-layered sandwiches	X: Rossmann-like domain in prismane-like proteins (From Topology)	H: Rossmann-like domain in prismane-like proteins (From Topology)	T: Rossmann-like domain in prismane-like proteins	F: Prismane_3rd	ECOD (1.6)
A	CODH	e6ondA3	A: few secondary structure elements	X: Fe-binding domain in prismane-like proteins (From Topology)	H: Fe-binding domain in prismane-like proteins (From Topology)	T: Fe-binding domain in prismane-like proteins	F: CODH	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.1270.30	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (utative)
D	3.40.50.2030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
C	1.20.1270.30	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (utative)
C	3.40.50.2030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
B	1.20.1270.30	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (utative)
B	3.40.50.2030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
A	1.20.1270.30	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (utative)
A	3.40.50.2030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03063	Prismane/CO dehydrogenase family (Prismane)	Prismane/CO dehydrogenase family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Carbon monoxide dehydrogenase	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding metal cluster binding peroxidase activity oxidoreductase activity antioxidant activity oxidoreductase activity, acting on peroxide as acceptor cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding metal cluster binding peroxidase activity oxidoreductase activity antioxidant activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity anaerobic carbon-monoxide dehydrogenase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor oxidoreductase activity, acting on the aldehyde or oxo group of donors hydroxylamine reductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors 4 iron, 4 sulfur cluster binding	metabolic process cellular process generation of precursor metabolites and energy response to hydrogen peroxide response to oxidative stress response to stimulus response to stress response to chemical response to oxygen-containing compound response to reactive oxygen species	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR016099	Prismane-like, alpha/beta-sandwich	Homologous Superfamily
A, B, C, D	IPR004137	Hydroxylamine reductase/Ni-containing CO dehydrogenase	Family
A, B, C, D	IPR016101	CO dehydrogenase, alpha-bundle	Homologous Superfamily
A, B, C, D	IPR010047	Ni-containing CO dehydrogenase	Family
A, B, C, D	IPR011254	Prismane-like superfamily	Homologous Superfamily

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.