4OZ6 | pdb_00004oz6

Structure of the Branched Intermediate in Protein Splicing

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	d4oz6a_	All beta proteins	Hedgehog/intein (Hint) domain	Hedgehog/intein (Hint) domain	Intein (protein splicing domain)	automated matches	(Mycobacterium xenopi ) [TaxId: 1789 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Hedgehog/intein (Hint) domain	8043149	3001979	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	PhyR_sigma-like	e4oz6A1	A: alpha bundles	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PhyR_sigma-like	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.16.10	Mainly Beta	Beta Complex	Endonuclease - Pi-scei	Chain A, domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Mxe gyrA intein	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 nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity ATP-dependent activity ATP-dependent activity, acting on DNA DNA negative supercoiling activity catalytic activity, acting on DNA DNA topoisomerase activity catalytic activity macromolecular conformation isomerase activity	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 chromosome organization 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 chromosome organization DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex
B	ALA-MET-ARG-TYR	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 nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity ATP-dependent activity ATP-dependent activity, acting on DNA DNA negative supercoiling activity catalytic activity, acting on DNA DNA topoisomerase activity catalytic activity macromolecular conformation isomerase activity	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 chromosome organization 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 chromosome organization DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036844	Hint domain superfamily	Homologous Superfamily
A	IPR050220	Type II DNA Topoisomerases	Family
A	IPR030934	Intein C-terminal splicing region	Conserved Site
A	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
A	IPR006141	Intein N-terminal splicing region	PTM
A	IPR003587	Hint domain N-terminal	Domain
A	IPR003586	Hint domain C-terminal	Domain
A	IPR002205	DNA topoisomerase, type IIA, domain A	Domain
B	IPR036844	Hint domain superfamily	Homologous Superfamily
B	IPR050220	Type II DNA Topoisomerases	Family
B	IPR030934	Intein C-terminal splicing region	Conserved Site
B	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
B	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
B	IPR006141	Intein N-terminal splicing region	PTM
B	IPR003587	Hint domain N-terminal	Domain
B	IPR003586	Hint domain C-terminal	Domain
B	IPR002205	DNA topoisomerase, type IIA, domain A	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.