4DTF | pdb_00004dtf

Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with AMP-PNP and Mg++

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	SCOP2B Superfamily	Glutamine synthetase/guanido kinase	8090901	3000676	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)
A	V-set	e4dtfA1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.3680.20	Mainly Alpha	Orthogonal Bundle	TerB-like	Actin cross-linking domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	VgrG protein	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding acid-amino acid ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity toxin activity	cellular component disassembly actin polymerization or depolymerization actin cytoskeleton organization protein-containing complex organization actin filament organization protein-containing complex disassembly actin filament depolymerization cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis supramolecular fiber organization protein depolymerization cellular component disassembly actin polymerization or depolymerization actin cytoskeleton organization protein-containing complex organization actin filament organization protein-containing complex disassembly actin filament depolymerization cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis supramolecular fiber organization protein depolymerization cytoskeleton organization peptidyl-glutamine modification peptidyl-lysine modification primary metabolic process isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine peptide cross-linking macromolecule modification peptidyl-amino acid modification isopeptide cross-linking metabolic process protein metabolic process macromolecule metabolic process protein modification process	cellular anatomical structure extracellular region host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region host cell cytosol other organism part host cell cytoplasm part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017847	Type VI secretion system, RhsGE-associated Vgr family subset	Family
A	IPR050708	Type VI secretion system VgrG/RHS	Family
A	IPR006533	Type VI secretion system, RhsGE-associated Vgr protein	Family
A	IPR032074	Actin cross-linking domain	Domain
A	IPR006531	Gp5/Type VI secretion system Vgr protein, OB-fold domain	Domain
A	IPR037026	Vgr protein, OB-fold domain superfamily	Homologous Superfamily
A	IPR054030	Gp5/Type VI secretion system Vgr, C-terminal trimerisation domain	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.