4GDF | pdb_00004gdf

A Crystal Structure of SV40 Large T Antigen

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)
F	SCOP2B Superfamily	RecA-like P-loop NTPases	8042358	3002019	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Origin of replication-binding domain, RBD-like	8041337	3001937	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Origin of replication-binding domain, RBD-like	8041337	3001937	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8042358	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8042358	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Origin of replication-binding domain, RBD-like	8041337	3001937	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8042358	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Origin of replication-binding domain, RBD-like	8041337	3001937	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)
F	Clenterotox	e4gdfF1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: Clenterotox	ECOD (v294.1)
F	PPV_E1_C	e4gdfF2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PPV_E1_C	ECOD (v294.1)
E	Clenterotox	e4gdfE1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: Clenterotox	ECOD (v294.1)
E	PPV_E1_C	e4gdfE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PPV_E1_C	ECOD (v294.1)
B	Clenterotox	e4gdfB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: Clenterotox	ECOD (v294.1)
B	PPV_E1_C	e4gdfB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PPV_E1_C	ECOD (v294.1)
A	Rhv	e4gdfA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Rhv	ECOD (v294.1)
A	PPV_E1_C	e4gdfA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PPV_E1_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
F	1.10.10.510	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Zinc finger, large T-antigen D1 domain	CATH (4.3.0)
F	1.20.1050.70	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	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)
E	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
E	1.10.10.510	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Zinc finger, large T-antigen D1 domain	CATH (4.3.0)
E	1.20.1050.70	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	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)
B	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
B	1.10.10.510	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Zinc finger, large T-antigen D1 domain	CATH (4.3.0)
B	1.20.1050.70	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	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)
A	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
A	1.10.10.510	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Zinc finger, large T-antigen D1 domain	CATH (4.3.0)
A	1.20.1050.70	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E, F	PF02217	Origin of replication binding protein (T_Ag_DNA_bind)	Origin of replication binding protein	This domain of large T antigen binds to the SV40 origin of DNA replication [1].	Domain
A, B, E, F	PF06431	Polyomavirus large T antigen C-terminus (Polyoma_lg_T_C)	Polyomavirus large T antigen C-terminus	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, H	DNA (32-MER)	-	-	-
C, G	DNA (32-MER)	-	-	-
A, B, E, F	Large T antigen	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin 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 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 cation binding transition metal ion binding zinc ion binding metal ion binding nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity 3'-5' DNA helicase activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA macromolecular conformation isomerase activity identical protein binding protein binding single-stranded DNA binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host JAK-STAT cascade symbiont-mediated perturbation of host process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host JAK-STAT cascade symbiont-mediated perturbation of host process symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process DNA biosynthetic process bidirectional double-stranded viral DNA replication symbiont-mediated perturbation of host ubiquitin-like protein modification symbiont-mediated perturbation of host cell cycle progression symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E, F	IPR001623	DnaJ domain	Domain
A, B, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, E, F	IPR017910	Zinc finger, large T-antigen D1-type	Domain
A, B, E, F	IPR003133	T antigen, Ori-binding	Domain
A, B, E, F	IPR037102	Zinc finger, large T-antigen D1 domain superfamily	Homologous Superfamily
A, B, E, F	IPR036869	Chaperone J-domain superfamily	Homologous Superfamily
A, B, E, F	IPR014015	Helicase, superfamily 3, DNA virus	Domain
A, B, E, F	IPR016392	Large T antigen, polyomaviridae	Family
A, B, E, F	IPR010932	Large T antigen, polyomavirus, C-terminal	Domain

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.