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
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)
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)
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)
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)
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)
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)
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)
J	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8034693	3000500	SCOP2B (2022-06-29)
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)
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)
G	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8037572	3001106	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)
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)
J	Acetyltransf_16	e4lylJ1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
P	Acetyltransf_16	e4lylP1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
N	Acetyltransf_16	e4lylN1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
L	Acetyltransf_16	e4lylL1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
H	Acetyltransf_16	e4lylH1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
F	Acetyltransf_16	e4lylF1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
D	Acetyltransf_16	e4lylD1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
B	Acetyltransf_16	e4lylB1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
G	Acetyltransf_16	e4lylG1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
O	Acetyltransf_16	e4lylO1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
M	Acetyltransf_16	e4lylM1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
K	Acetyltransf_16	e4lylK1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
I	Acetyltransf_16	e4lylI1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
E	Acetyltransf_16	e4lylE1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
C	Acetyltransf_16	e4lylC1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)
A	Acetyltransf_16	e4lylA1	A: alpha arrays	X: Alpha-beta plaits	H: HTH	T: winged helix domain	F: Acetyltransf_16	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	3.10.450.20	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
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)
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)
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)
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)
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)

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

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

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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.