2YCL | pdb_00002ycl

complete structure of the corrinoid,iron-sulfur protein including the N-terminal domain with a 4Fe-4S cluster

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	CdhD-like	8051756	4007502	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Dihydropteroate synthetase-like	8089867	3000643	SCOP2 (2022-06-29)
A	SCOP2 Family	AcsC Fe-S domain-like	8045247	4004371	SCOP2 (2022-06-29)
A	SCOP2 Family	CdhD-like	8089864	4007502	SCOP2 (2022-06-29)
A	SCOP2 Family	AcsC cobalamin-binding domain	8089869	4007687	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	AcsC Fe-S domain-like	8089863	3002395	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Dihydropteroate synthetase-like	8089865	3000643	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	AcsC C-terminal domain-like	8089866	3002396	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)
B		e2yclB1	A: Thioredoxin-like	X: Thioredoxin-like	H: Thioredoxin-like	T: CdhD	F:	ECOD (20:10:01)
A		e2yclA1	A: Ribonuclease H-like	X: Ribonuclease H-like	H: Ribonuclease H-like	T: CdhD	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.20.20	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Dihydropteroate synthase-like	CATH (4.3.0)
A	3.20.20.20	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Dihydropteroate synthase-like	CATH (4.3.0)
A	3.40.50.11600	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF03599	CO dehydrogenase/acetyl-CoA synthase delta subunit (CdhD)	CO dehydrogenase/acetyl-CoA synthase delta subunit	-	Family
A	PF04060	Putative Fe-S cluster (FeS)	Putative Fe-S cluster	This family includes a domain with four conserved cysteines that probably form an Fe-S redox cluster.	Domain
A	PF03599	CO dehydrogenase/acetyl-CoA synthase delta subunit (CdhD)	CO dehydrogenase/acetyl-CoA synthase delta subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN	-	-	-
A	CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding	nucleoside phosphate metabolic process catabolic process organophosphate catabolic process primary metabolic process purine-containing compound catabolic process nucleoside phosphate catabolic process acetyl-CoA metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound catabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process catabolic process organophosphate catabolic process primary metabolic process purine-containing compound catabolic process nucleoside phosphate catabolic process acetyl-CoA metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound catabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process phosphorus metabolic process acetyl-CoA catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR016041	CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel	Domain
B	IPR011005	Dihydropteroate synthase-like superfamily	Homologous Superfamily
B	IPR051069	Acetyl-CoA decarbonylase/synthase complex subunit	Family
A	IPR016218	Acetyl-CoA decarbonylase/synthase complex, gamma subunit	Family
A	IPR016041	CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel	Domain
A	IPR007202	4Fe-4S domain	Domain
A	IPR011005	Dihydropteroate synthase-like superfamily	Homologous Superfamily
A	IPR051069	Acetyl-CoA decarbonylase/synthase complex subunit	Family

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.