3HHQ | pdb_00003hhq

Crystal structure of apo dUT1p from Saccharomyces cerevisiae

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)
X	d3hhqx_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
W	d3hhqw_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
V	d3hhqv_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
U	d3hhqu_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
T	d3hhqt_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
S	d3hhqs_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
R	d3hhqr_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
Q	d3hhqq_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
P	d3hhqp_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
O	d3hhqo_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
N	d3hhqn_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
M	d3hhqm_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
L	d3hhql_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
K	d3hhqk_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
J	d3hhqj_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
I	d3hhqi_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
H	d3hhqh_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G	d3hhqg_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F	d3hhqf_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d3hhqe_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d3hhqd_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d3hhqc_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3hhqb_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d3hhqa_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
X	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
W	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	dUTPase-like	8073090	3001957	SCOP2B (2022-06-29)
B	SCOP2 Family	dUTPase-like	8073089	4002970	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	dUTPase-like	8073090	3001957	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	dUTPase-like	8073090	3001957	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)
X	YgbB	e3hhqX1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
W	YgbB	e3hhqW1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
V	YgbB	e3hhqV1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
U	YgbB	e3hhqU1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
T	YgbB	e3hhqT1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
S	YgbB	e3hhqS1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
R	YgbB	e3hhqR1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
Q	YgbB	e3hhqQ1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
P	YgbB	e3hhqP1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
O	YgbB	e3hhqO1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
N	YgbB	e3hhqN1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
M	YgbB	e3hhqM1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
L	YgbB	e3hhqL1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
K	YgbB	e3hhqK1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
J	YgbB	e3hhqJ1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
I	YgbB	e3hhqI1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
H	YgbB	e3hhqH1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
G	YgbB	e3hhqG1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
F	YgbB	e3hhqF1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
E	YgbB	e3hhqE1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
D	YgbB	e3hhqD1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
C	YgbB	e3hhqC1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
B	YgbB	e3hhqB1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295.2)
A	Ppx-GppA	e3hhqA1	A: alpha arrays	X: Alpha-beta plaits	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ppx-GppA	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
X	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
W	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
V	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
U	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
T	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
S	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
R	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
Q	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
P	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
O	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
N	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
M	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
L	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
K	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
J	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
I	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
H	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
G	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
F	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
E	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
D	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
C	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
B	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
A	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	PF00692	dUTPase (dUTPase)	dUTPase	dUTPase hydrolyses dUTP to dUMP and pyrophosphate.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	Deoxyuridine 5'-triphosphate nucleotidohydrolase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pyrophosphatase activity dITP diphosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity dUTP diphosphatase activity	pyrimidine deoxyribonucleotide metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine deoxyribonucleoside monophosphate metabolic process nucleobase-containing compound metabolic process pyrimidine deoxyribonucleotide biosynthetic process nucleobase-containing small molecule metabolic process deoxyribonucleoside monophosphate biosynthetic process small molecule metabolic process pyrimidine deoxyribonucleoside monophosphate biosynthetic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process pyrimidine deoxyribonucleotide metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine deoxyribonucleoside monophosphate metabolic process nucleobase-containing compound metabolic process pyrimidine deoxyribonucleotide biosynthetic process nucleobase-containing small molecule metabolic process deoxyribonucleoside monophosphate biosynthetic process small molecule metabolic process pyrimidine deoxyribonucleoside monophosphate biosynthetic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process nucleoside monophosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process 2'-deoxyribonucleotide biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process dUMP biosynthetic process nucleoside monophosphate biosynthetic process dUMP metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process pyrimidine nucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process catabolic process pyrimidine nucleoside triphosphate metabolic process organophosphate catabolic process pyrimidine nucleoside triphosphate catabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process pyrimidine deoxyribonucleoside triphosphate metabolic process pyrimidine deoxyribonucleoside triphosphate catabolic process purine nucleoside triphosphate catabolic process purine deoxyribonucleoside triphosphate metabolic process deoxyribose phosphate catabolic process purine nucleotide metabolic process purine deoxyribonucleoside triphosphate catabolic process nucleotide catabolic process deoxyribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process purine deoxyribonucleotide catabolic process carbohydrate derivative catabolic process purine-containing compound catabolic process deoxyribonucleoside triphosphate catabolic process purine-containing compound metabolic process dITP catabolic process purine deoxyribonucleotide metabolic process pyrimidine deoxyribonucleotide catabolic process pyrimidine-containing compound catabolic process dUTP metabolic process pyrimidine nucleotide catabolic process dUTP catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	IPR008181	Deoxyuridine triphosphate nucleotidohydrolase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	IPR033704	dUTPase, trimeric	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	IPR036157	dUTPase-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	IPR029054	dUTPase-like	Domain