6DRT | pdb_00006drt

Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4

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)
C	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA clamp	8036423	3000780	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)
C	DNA_PPF_1	e6drtC1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_PPF_1	ECOD (1.6)
C	gp45-slide_C	e6drtC2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: gp45-slide_C	ECOD (1.6)
B	DNA_PPF_1	e6drtB1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_PPF_1	ECOD (1.6)
B	gp45-slide_C	e6drtB2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: gp45-slide_C	ECOD (1.6)
A	DNA_PPF_1	e6drtA2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_PPF_1	ECOD (1.6)
A	gp45-slide_C	e6drtA1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: gp45-slide_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
B	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
A	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF09116	gp45 sliding clamp, C terminal (gp45-slide_C)	gp45 sliding clamp, C terminal	Members of this family are essential for the interaction of the gp45 sliding clamp with the corresponding polymerase. They adopt a DNA clamp fold, consisting of two alpha helices and two beta sheets - the fold is duplicated and has internal pseudo tw ...	Members of this family are essential for the interaction of the gp45 sliding clamp with the corresponding polymerase. They adopt a DNA clamp fold, consisting of two alpha helices and two beta sheets - the fold is duplicated and has internal pseudo two-fold symmetry [1].	Domain
A, B, C	PF02916	DNA polymerase processivity factor (DNA_PPF)	DNA polymerase processivity factor		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E, F	GP45 recognition loop	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 ligase activity, forming phosphoric ester bonds catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase activity ligase activity cation binding metal ion binding DNA ligase (ATP) 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 cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair DNA recombination	-
A, B, C	DNA polymerase clamp	enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator 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 viral gene expression viral process viral transcription viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic 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 viral gene expression viral process viral transcription viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication bidirectional double-stranded viral DNA replication DNA biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, E, F	IPR016059	DNA ligase, ATP-dependent, conserved site	Conserved Site
D, E, F	IPR012310	DNA ligase, ATP-dependent, central	Domain
D, E, F	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
D, E, F	IPR050326	NAD-dependent DNA ligase B	Family
A, B, C	IPR046938	DNA clamp superfamily	Homologous Superfamily
A, B, C	IPR046389	Sliding clamp	Family
A, B, C	IPR004190	DNA polymerase processivity factor	Domain
A, B, C	IPR015200	Sliding clamp, 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.