2FCC | pdb_00002fcc

Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth B]	d2fccb_	All alpha proteins	T4 endonuclease V	T4 endonuclease V	T4 endonuclease V	T4 endonuclease V	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
E [auth A]	d2fcca_	All alpha proteins	T4 endonuclease V	T4 endonuclease V	T4 endonuclease V	T4 endonuclease V	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth B]	SCOP2B Superfamily	T4 endonuclease V	8036751	3001328	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	T4 endonuclease V	8036751	3001328	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)
F [auth B]	Globin	e2fccB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: Globin	ECOD (v294.1)
E [auth A]	Globin	e2fccA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: Globin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth B]	1.10.440.10	Mainly Alpha	Orthogonal Bundle	Endonuclease V	T4 endonuclease V	CATH (4.3.0)
E [auth A]	1.10.440.10	Mainly Alpha	Orthogonal Bundle	Endonuclease V	T4 endonuclease V	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B]	PF03013	Pyrimidine dimer DNA glycosylase (Pyr_excise)	Pyrimidine dimer DNA glycosylase	Pyrimidine dimer DNA glycosylases excise pyrimidine dimers by hydrolysis of the glycosylic bond of the 5' pyrimidine, followed by the intra-pyrimidine phosphodiester bond. Pyrimidine dimers are the major UV-lesions of DNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth A], F [auth B]	Endonuclease V	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 pyrimidine dimer DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds 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 pyrimidine dimer DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds deoxyribodipyrimidine endonucleosidase activity	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	-
B [auth D], D [auth F]	DNA (5'-D(GPGPCP(BRU)P(BRU)PCPAP(BRU)PCPCP(BRU)PGP*G)-3')	-	-	-
A [auth C], C [auth E]	DNA (5'-D(CPCPAPGPGPAP(PED)PGPAPAPGPCP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR024796	T4 endonuclease V	Homologous Superfamily
E [auth A], F [auth B]	IPR004260	Pyrimidine dimer DNA glycosylase	Family
E [auth A], F [auth B]	IPR021143	Pyrimidine dimer DNA glycosylase, endonuclease V type	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth D], D [auth F]	BRU	Parent Component: DU
A [auth C], C [auth E]	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.