1JQK | pdb_00001jqk

Crystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum

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)
F	d1jqkf_	Multi-domain proteins (alpha and beta)	Prismane protein-like	Prismane protein-like	Carbon monoxide dehydrogenase	Ni-containing carbon monoxide dehydrogenase	(Rhodospirillum rubrum ) [TaxId: 1085 ],	SCOPe (2.08)
E	d1jqke_	Multi-domain proteins (alpha and beta)	Prismane protein-like	Prismane protein-like	Carbon monoxide dehydrogenase	Ni-containing carbon monoxide dehydrogenase	(Rhodospirillum rubrum ) [TaxId: 1085 ],	SCOPe (2.08)
D	d1jqkd_	Multi-domain proteins (alpha and beta)	Prismane protein-like	Prismane protein-like	Carbon monoxide dehydrogenase	Ni-containing carbon monoxide dehydrogenase	(Rhodospirillum rubrum ) [TaxId: 1085 ],	SCOPe (2.08)
C	d1jqkc_	Multi-domain proteins (alpha and beta)	Prismane protein-like	Prismane protein-like	Carbon monoxide dehydrogenase	Ni-containing carbon monoxide dehydrogenase	(Rhodospirillum rubrum ) [TaxId: 1085 ],	SCOPe (2.08)
B	d1jqkb_	Multi-domain proteins (alpha and beta)	Prismane protein-like	Prismane protein-like	Carbon monoxide dehydrogenase	Ni-containing carbon monoxide dehydrogenase	(Rhodospirillum rubrum ) [TaxId: 1085 ],	SCOPe (2.08)
A	d1jqka_	Multi-domain proteins (alpha and beta)	Prismane protein-like	Prismane protein-like	Carbon monoxide dehydrogenase	Ni-containing carbon monoxide dehydrogenase	(Rhodospirillum rubrum ) [TaxId: 1085 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Prismane protein N-terminal helical bundle-like	8055594	3002294	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Prismane protein cluster-binding domain-like	8037257	3001926	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Prismane protein cluster-binding domain-like	8055593	3001926	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Prismane protein cluster-binding domain-like	8055593	3001926	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Prismane protein N-terminal helical bundle-like	8055594	3002294	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Prismane protein cluster-binding domain-like	8037257	3001926	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Prismane protein cluster-binding domain-like	8037257	3001926	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Prismane protein N-terminal helical bundle-like	8055594	3002294	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Prismane protein cluster-binding domain-like	8055593	3001926	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Prismane protein N-terminal helical bundle-like	8055594	3002294	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Prismane protein cluster-binding domain-like	8037257	3001926	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Prismane protein cluster-binding domain-like	8055593	3001926	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Prismane protein cluster-binding domain-like	8037257	3001926	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Prismane protein cluster-binding domain-like	8055593	3001926	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Prismane protein N-terminal helical bundle-like	8055594	3002294	SCOP2B (2022-06-29)
A	SCOP2 Family	Carbon monoxide dehydrogenase	8024878	4003730	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Prismane protein cluster-binding domain-like	8055593	3001926	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Prismane protein cluster-binding domain-like	8037257	3001926	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Prismane protein N-terminal helical bundle-like	8055594	3002294	SCOP2 (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	Ribonuc_L-PSP	e1jqkF5	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: Ribonuc_L-PSP	ECOD (develop294)
E	Ribonuc_L-PSP	e1jqkE5	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: Ribonuc_L-PSP	ECOD (develop294)
D	Ribonuc_L-PSP	e1jqkD5	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: Ribonuc_L-PSP	ECOD (develop294)
C	MR_MLE_N	e1jqkC1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: MR_MLE_N	ECOD (develop294)
B	Ribonuc_L-PSP	e1jqkB5	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: Ribonuc_L-PSP	ECOD (develop294)
A	ALO	e1jqkA5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ALO	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.2030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
F	1.20.1270.30	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
E	3.40.50.2030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
E	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)
D	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)
C	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)
B	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)
A	1.20.1270.30	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	carbon monoxide dehydrogenase	oxidoreductase activity catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron ion binding ferrous iron binding identical protein binding protein binding protein homodimerization activity oxidoreductase activity catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron ion binding ferrous iron binding identical protein binding protein binding protein homodimerization activity protein dimerization activity peroxidase activity antioxidant activity oxidoreductase activity, acting on peroxide 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, acting on the aldehyde or oxo group of donors iron-sulfur cluster binding 3 iron, 4 sulfur cluster binding metal cluster binding 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	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR016099	Prismane-like, alpha/beta-sandwich	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR004137	Hydroxylamine reductase/Ni-containing CO dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F	IPR016101	CO dehydrogenase, alpha-bundle	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR010047	Ni-containing CO dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.