8D2M | pdb_00008d2m

Covalent Schiff base complex of YedK C2A and abasic DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
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	BB1717-like	8059018	3000864	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	BB1717-like	8059018	3000864	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	F_UNCLASSIFIED	e8d2mA1	A: a+b complex topology	X: BB1717-like (From Topology)	H: BB1717-like (From Topology)	T: BB1717-like	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth B]	F_UNCLASSIFIED	e8d2mB1	A: a+b complex topology	X: BB1717-like (From Topology)	H: BB1717-like (From Topology)	T: BB1717-like	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF02586	SOS response associated peptidase (SRAP) (SRAP)	SOS response associated peptidase (SRAP)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	Abasic site processing protein YedK	lyase activity protein-DNA covalent cross-linking activity catalytic activity peptidase activity catalytic activity, acting on a protein hydrolase activity DNA binding binding single-stranded DNA binding nucleic acid binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process protein-DNA covalent cross-linking repair metabolic process macromolecule metabolic process DNA repair cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process protein-DNA covalent cross-linking repair metabolic process macromolecule metabolic process DNA repair SOS response proteolysis protein metabolic process	-
B [auth C], D	DNA (5'-D(GPTPCP(PED)PGPGP*A)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR003738	SOS response associated peptidase (SRAP)	Family
A, C [auth B]	IPR036590	SOS response associated peptidase-like	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth C], D	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.