6DC2 | pdb_00006dc2

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase C301S variant

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	e6dc2D4	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	e6dc2D1	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	e6dc2D3	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	e6dc2D2	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	e6dc2C4	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	e6dc2C1	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	e6dc2C3	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	e6dc2C2	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	e6dc2B3	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	e6dc2B4	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	e6dc2B2	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	e6dc2B1	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	e6dc2A1	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	e6dc2A3	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	e6dc2A2	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	e6dc2A4	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 (4.3.0)
D	3.40.50.2030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	1.20.1270.30	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
C	3.40.50.2030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	1.20.1270.30	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
B	3.40.50.2030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	1.20.1270.30	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
A	3.40.50.2030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

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.