7P9Z | pdb_00007p9z

Crystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing adenine opposite to lesion)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DNA-glycosylase	8107826	3000905	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		e7p9zA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F:	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth I]	DNA (5'-D(APGPAPAPAPAPAPAP*A)-3')	-	-	-
B	DNA (5'-D(TPTPTP(PED)TPTPTPCP*T)-3')	-	-	-
A	N-glycosylase/DNA lyase	DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds oxidized base lesion DNA N-glycosylase activity hydrolase activity DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds oxidized base lesion DNA N-glycosylase activity hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015254	N-glycosylase/DNA lyase-like	Family
A	IPR016544	N-glycosylase/DNA lyase	Family
A	IPR011257	DNA glycosylase	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	PED	RESID: AA0494 PSI-MOD : N-(DNA-1',2'-dideoxyribos-1'-ylidene)-L-prolinium MOD:01454

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.

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