2QBY | pdb_00002qby

Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S. solfataricus)

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 [auth B]		e2qbyB3	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: Clp_N	F:	ECOD (20:10:01)
C [auth A]		e2qbyA2	A: Profilin-like	X: sensor domains	H: sensor domains	T: PDZ	F:	ECOD (20:10:01)
C [auth A]		e2qbyA1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: AmoC	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D [auth B]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C [auth A]	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C [auth A]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C [auth A]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth B]	PF09079	CDC6, C terminal winged helix domain (WHD_Cdc6)	CDC6, C terminal winged helix domain	The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, how ...	The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity [1].	Domain
D [auth B]	PF22703	Cdc6 AAA+ ATPase-type lid domain (Cdc6_lid)	Cdc6 AAA+ ATPase-type lid domain	This domain is found in Cdc6 and related proteins. Cdc6 is a key protein involved in the pre-replication complex assembly. It contains AAA+ ATPase domain that is capped by a lid domain, represented by this entry [1-2].	Domain
D [auth B]	PF13401	AAA domain (AAA_22)	AAA domain		Domain
C [auth A]	PF09079	CDC6, C terminal winged helix domain (WHD_Cdc6)	CDC6, C terminal winged helix domain	The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, how ...	The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity [1].	Domain
C [auth A]	PF22703	Cdc6 AAA+ ATPase-type lid domain (Cdc6_lid)	Cdc6 AAA+ ATPase-type lid domain	This domain is found in Cdc6 and related proteins. Cdc6 is a key protein involved in the pre-replication complex assembly. It contains AAA+ ATPase domain that is capped by a lid domain, represented by this entry [1-2].	Domain
C [auth A]	PF13401	AAA domain (AAA_22)	AAA domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth B]	Cell division control protein 6 homolog 3	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	-
C [auth A]	Cell division control protein 6 homolog 1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	-
B [auth D]	DNA (33-MER)	-	-	-
A [auth C]	DNA (33-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth B]	IPR015163	Cdc6, C-terminal	Domain
D [auth B]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
D [auth B]	IPR050311	Origin recognition complex 1/Cell division control protein 6	Family
D [auth B]	IPR055237	Cdc6, AAA+ ATPase-type lid domain	Domain
D [auth B]	IPR014277	Orc1/Cdc6-type DNA replication protein, archaea	Family
D [auth B]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
D [auth B]	IPR049945	ORC1/DEAH AAA+ ATPase domain	Domain
D [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C [auth A]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C [auth A]	IPR014277	Orc1/Cdc6-type DNA replication protein, archaea	Family
C [auth A]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
C [auth A]	IPR015163	Cdc6, C-terminal	Domain
C [auth A]	IPR003593	AAA+ ATPase domain	Domain
C [auth A]	IPR050311	Origin recognition complex 1/Cell division control protein 6	Family
C [auth A]	IPR055237	Cdc6, AAA+ ATPase-type lid domain	Domain
C [auth A]	IPR049945	ORC1/DEAH AAA+ ATPase domain	Domain
C [auth A]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.