3IKL | pdb_00003ikl

Crystal structure of Pol gB delta-I4.

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3iklb1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	Class II aaRS ABD-related	Anticodon-binding domain of Class II aaRS	The aaRS-like accessory subunit of mitochondrial polymerase gamma, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ikla1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	Class II aaRS ABD-related	Anticodon-binding domain of Class II aaRS	The aaRS-like accessory subunit of mitochondrial polymerase gamma, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Class II aaRS ABD-related	8041652	3000465	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8041653	3000058	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS ABD-related	8041652	3000465	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8041653	3000058	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)
B	Sdh_cyt	e3iklB2	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Sdh_cyt	ECOD (v294.1)
B		e3iklB3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (v294.1)
A	Stap_Strp_tox_C	e3iklA2	A: a/b three-layered sandwiches	X: Retrovirus capsid protein	H: Ubiquitin-related	T: Ubiquitin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
A		e3iklA3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
A	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03129	Anticodon binding domain (HGTP_anticodon)	Anticodon binding domain	This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [1] it is probably the anticodon binding domain [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA polymerase subunit gamma-2, mitochondrial	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding double-stranded DNA binding binding nucleic acid binding enzyme regulator activity DNA polymerase processivity factor activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding double-stranded DNA binding binding nucleic acid binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity protein binding DNA polymerase binding enzyme binding identical protein binding	regulation of cellular process regulation of catalytic activity positive regulation of biological process regulation of transferase activity regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of molecular function positive regulation of metabolic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of cellular process regulation of catalytic activity positive regulation of biological process regulation of transferase activity regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of molecular function positive regulation of metabolic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process biological regulation positive regulation of catalytic activity positive regulation of DNA biosynthetic process primary metabolic process regulation of macromolecule metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulation of molecular function positive regulation of DNA metabolic process biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process DNA biosynthetic process positive regulation of DNA-directed DNA polymerase activity regulation of DNA metabolic process DNA-templated DNA replication DNA replication mitochondrial DNA metabolic process mitochondrial DNA replication cellular component organization organelle organization cellular component organization or biogenesis mitochondrion organization developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial protein-containing complex protein-containing complex catalytic complex membrane-enclosed lumen transferase complex mitochondrial matrix membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial protein-containing complex protein-containing complex catalytic complex membrane-enclosed lumen transferase complex mitochondrial matrix DNA polymerase complex intracellular organelle lumen transferase complex, transferring phosphorus-containing groups organelle lumen gamma DNA polymerase complex intracellular protein-containing complex intracellular membraneless organelle nucleoid membraneless organelle mitochondrial nucleoid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B	IPR004154	Anticodon-binding	Domain
A, B	IPR042064	POLG2, C-terminal	Domain
A, B	IPR036621	Anticodon-binding domain superfamily	Homologous Superfamily
A, B	IPR027031	Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9UHN1	progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4 progressive external ophthalmoplegia progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1 large cell medulloblastoma Mitochondrial Diseases muscular disease rhabdomyolysis leukodystrophy mitochondrial DNA depletion syndrome 4a myopathy medulloblastoma muscle tissue disease osteosarcoma

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.