4LYL | pdb_00004lyl

Crystal structure of uracil-DNA glycosylase from cod (Gadus morhua) in complex with the proteinaceous inhibitor UGI

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
P	d4lylp_	Alpha and beta proteins (a+b)	Cystatin-like	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	(Bacillus phage PBS2 ) [TaxId: 10684 ],	SCOPe (2.08)
N	d4lyln_	Alpha and beta proteins (a+b)	Cystatin-like	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	(Bacillus phage PBS2 ) [TaxId: 10684 ],	SCOPe (2.08)
L	d4lyll_	Alpha and beta proteins (a+b)	Cystatin-like	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	(Bacillus phage PBS2 ) [TaxId: 10684 ],	SCOPe (2.08)
J	d4lylj_	Alpha and beta proteins (a+b)	Cystatin-like	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	(Bacillus phage PBS2 ) [TaxId: 10684 ],	SCOPe (2.08)
H	d4lylh_	Alpha and beta proteins (a+b)	Cystatin-like	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	(Bacillus phage PBS2 ) [TaxId: 10684 ],	SCOPe (2.08)
F	d4lylf_	Alpha and beta proteins (a+b)	Cystatin-like	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	(Bacillus phage PBS2 ) [TaxId: 10684 ],	SCOPe (2.08)
D	d4lyld_	Alpha and beta proteins (a+b)	Cystatin-like	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	(Bacillus phage PBS2 ) [TaxId: 10684 ],	SCOPe (2.08)
B	d4lylb_	Alpha and beta proteins (a+b)	Cystatin-like	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	Uracil-DNA glycosylase inhibitor protein	(Bacillus phage PBS2 ) [TaxId: 10684 ],	SCOPe (2.08)
O	d4lylo1	Alpha and beta proteins (a/b)	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase	Uracil-DNA glycosylase	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
O	d4lylo2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
M	d4lylm1	Alpha and beta proteins (a/b)	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase	Uracil-DNA glycosylase	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
M	d4lylm2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
K	d4lylk1	Alpha and beta proteins (a/b)	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase	Uracil-DNA glycosylase	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
K	d4lylk2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
I	d4lyli1	Alpha and beta proteins (a/b)	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase	Uracil-DNA glycosylase	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
I	d4lyli2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
G	d4lylg1	Alpha and beta proteins (a/b)	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase	Uracil-DNA glycosylase	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
G	d4lylg2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
E	d4lyle1	Alpha and beta proteins (a/b)	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase	Uracil-DNA glycosylase	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
E	d4lyle2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
C	d4lylc1	Alpha and beta proteins (a/b)	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase	Uracil-DNA glycosylase	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
C	d4lylc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
A	d4lyla1	Alpha and beta proteins (a/b)	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase	Uracil-DNA glycosylase	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
A	d4lyla2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8034693	3000500	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8034693	3000500	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8034693	3000500	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8034693	3000500	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8034693	3000500	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8034693	3000500	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8034693	3000500	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8034693	3000500	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8037572	3001106	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8037572	3001106	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8037572	3001106	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8037572	3001106	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8037572	3001106	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8037572	3001106	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8037572	3001106	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8037572	3001106	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)
P	EUF08292	e4lylP1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: EUF08292	ECOD (1.6)
N	EUF08292	e4lylN1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: EUF08292	ECOD (1.6)
L	EUF08292	e4lylL1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: EUF08292	ECOD (1.6)
J	EUF08292	e4lylJ1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: EUF08292	ECOD (1.6)
H	EUF08292	e4lylH1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: EUF08292	ECOD (1.6)
F	EUF08292	e4lylF1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: EUF08292	ECOD (1.6)
D	EUF08292	e4lylD1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: EUF08292	ECOD (1.6)
B	EUF08292	e4lylB1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: EUF08292	ECOD (1.6)
O	UDG	e4lylO1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
M	UDG	e4lylM1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
K	UDG	e4lylK1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
I	UDG	e4lylI1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
G	UDG	e4lylG1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
E	UDG	e4lylE1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
C	UDG	e4lylC1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
A	UDG	e4lylA1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	3.10.450.20	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
N	3.10.450.20	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
L	3.10.450.20	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
J	3.10.450.20	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
H	3.10.450.20	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
F	3.10.450.20	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
D	3.10.450.20	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
B	3.10.450.20	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
O	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (4.3.0)
M	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (4.3.0)
K	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (4.3.0)
I	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (4.3.0)
G	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (4.3.0)
E	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (4.3.0)
C	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (4.3.0)
A	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K, M, O	PF03167	Uracil DNA glycosylase superfamily (UDG)	Uracil DNA glycosylase superfamily		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L, N, P	Uracil-DNA glycosylase inhibitor	-	-	-
A, C, E, G, I A, C, E, G, I, K, M, O	Uracil-DNA glycosylase	uracil DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds deaminated base DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity	cellular response to stimulus response to stimulus base-excision repair, AP site formation via deaminated base removal 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 cellular response to stimulus response to stimulus base-excision repair, AP site formation via deaminated base removal 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 base-excision repair, AP site formation DNA repair	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L, N, P	IPR024062	Bacteriophage PBS2, uracil-glycosylase inhibitor	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR043805	Uracil-DNA glycosylase inhibitor	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR002043	Uracil-DNA glycosylase family 1	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR018085	Uracil-DNA glycosylase, active site	Active Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR036895	Uracil-DNA glycosylase-like domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR005122	Uracil-DNA glycosylase-like	Domain