1IQP

Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1iqpd1	All alpha proteins	post-AAA+ oligomerization domain-like	post-AAA+ oligomerization domain-like	DNA polymerase III clamp loader subunits, C-terminal domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
D	d1iqpd2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
A	d1iqpa1	All alpha proteins	post-AAA+ oligomerization domain-like	post-AAA+ oligomerization domain-like	DNA polymerase III clamp loader subunits, C-terminal domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
A	d1iqpa2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
B	d1iqpb1	All alpha proteins	post-AAA+ oligomerization domain-like	post-AAA+ oligomerization domain-like	DNA polymerase III clamp loader subunits, C-terminal domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
B	d1iqpb2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
C	d1iqpc1	All alpha proteins	post-AAA+ oligomerization domain-like	post-AAA+ oligomerization domain-like	DNA polymerase III clamp loader subunits, C-terminal domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
C	d1iqpc2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
E	d1iqpe1	All alpha proteins	post-AAA+ oligomerization domain-like	post-AAA+ oligomerization domain-like	DNA polymerase III clamp loader subunits, C-terminal domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
E	d1iqpe2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
F	d1iqpf1	All alpha proteins	post-AAA+ oligomerization domain-like	post-AAA+ oligomerization domain-like	DNA polymerase III clamp loader subunits, C-terminal domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
F	d1iqpf2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication factor C	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8034163	3000691	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104161	3002834	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8034164	3002019	SCOP2B (2022-06-29)
A	SCOP2 Family	DNA polymerase III clamp loader subunits, C-terminal domain	8021783	4001080	SCOP2 (2022-06-29)
A	SCOP2 Family	Extended AAA-ATPase domain	8021784	4000283	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Post-AAA+ oligomerization domain-like	8034163	3000691	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8034164	3002019	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104161	3002834	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8034163	3000691	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104161	3002834	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8034164	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8034164	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8034163	3000691	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104161	3002834	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8034164	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104161	3002834	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8034163	3000691	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104161	3002834	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8034163	3000691	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RecA-like P-loop NTPases	8034164	3002019	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Rep_fac_C	e1iqpD1	A: alpha arrays	X: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	H: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	T: DNA polymerase III clamp loader subunits, C-terminal domain	F: Rep_fac_C	ECOD (1.6)
D	AAA_assoc_2_1	e1iqpD5	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_assoc_2_1	ECOD (1.6)
D	Sigma54_activat	e1iqpD4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
A	Rep_fac_C	e1iqpA1	A: alpha arrays	X: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	H: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	T: DNA polymerase III clamp loader subunits, C-terminal domain	F: Rep_fac_C	ECOD (1.6)
A	AAA_assoc_2_1	e1iqpA2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_assoc_2_1	ECOD (1.6)
A	Sigma54_activat	e1iqpA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
B	Rep_fac_C	e1iqpB1	A: alpha arrays	X: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	H: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	T: DNA polymerase III clamp loader subunits, C-terminal domain	F: Rep_fac_C	ECOD (1.6)
B	AAA_assoc_2_1	e1iqpB5	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_assoc_2_1	ECOD (1.6)
B	Sigma54_activat	e1iqpB4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
C	Rep_fac_C	e1iqpC1	A: alpha arrays	X: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	H: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	T: DNA polymerase III clamp loader subunits, C-terminal domain	F: Rep_fac_C	ECOD (1.6)
C	AAA_assoc_2_1	e1iqpC5	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_assoc_2_1	ECOD (1.6)
C	Sigma54_activat	e1iqpC4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
E	Rep_fac_C	e1iqpE1	A: alpha arrays	X: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	H: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	T: DNA polymerase III clamp loader subunits, C-terminal domain	F: Rep_fac_C	ECOD (1.6)
E	AAA_assoc_2_1	e1iqpE5	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_assoc_2_1	ECOD (1.6)
E	Sigma54_activat	e1iqpE4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
F	Rep_fac_C	e1iqpF1	A: alpha arrays	X: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	H: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	T: DNA polymerase III clamp loader subunits, C-terminal domain	F: Rep_fac_C	ECOD (1.6)
F	AAA_assoc_2_1	e1iqpF5	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_assoc_2_1	ECOD (1.6)
F	Sigma54_activat	e1iqpF4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
E	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
F	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF08542	Replication factor C C-terminal domain (Rep_fac_C)	Replication factor C C-terminal domain	This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which resul ...	This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A [1].	Domain
A, B, C, D, E A, B, C, D, E, F	PF00004	ATPase family associated with various cellular activities (AAA) (AAA)	ATPase family associated with various cellular activities (AAA)	AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].	Domain

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	RFCS	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA clamp loader activity catalytic activity ATP-dependent activity 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 endonuclease activity nuclease activity hydrolase activity, acting on ester bonds	intein-mediated protein splicing primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process protein splicing cellular response to stimulus intein-mediated protein splicing primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process protein splicing cellular response to stimulus response to stimulus DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress DNA repair DNA-templated DNA replication DNA replication	intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure DNA replication factor C complex organelle membraneless organelle replication fork intracellular membraneless organelle chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR050238	DNA Replication and Repair Clamp Loader Complex	Family
A, B, C, D, E A, B, C, D, E, F	IPR036844	Hint domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR008921	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR013748	Replication factor C, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR030934	Intein C-terminal splicing region	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR006142	Intein	Domain
A, B, C, D, E A, B, C, D, E, F	IPR004042	Intein DOD homing endonuclease, central region	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027434	Homing endonuclease	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006141	Intein N-terminal splicing region	PTM
A, B, C, D, E A, B, C, D, E, F	IPR047854	Replication factor C, lid domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR004860	Homing endonuclease, LAGLIDADG domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003959	ATPase, AAA-type, core	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003587	Hint domain N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003586	Hint domain C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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1IQP

Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage