1W4R | pdb_00001w4r

Structure of a type II thymidine kinase with bound dTTP

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1w4rb1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1w4rb2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1w4rc1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1w4rc2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1w4rd1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1w4rd2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1w4re1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1w4re2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1w4rf1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1w4rf2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d1w4rh1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d1w4rh2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d1w4rg1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d1w4rg2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1w4ra1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1w4ra2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8089737	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8089738	3000068	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8089738	3000068	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8089737	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8089738	3000068	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8089737	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8089737	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8089738	3000068	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8089738	3000068	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RecA-like P-loop NTPases	8089737	3002019	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8089738	3000068	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RecA-like P-loop NTPases	8089737	3002019	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RecA-like P-loop NTPases	8089737	3002019	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8089738	3000068	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8089738	3000068	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8089737	3002019	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)
B	Clp_N	e1w4rB3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Clp_N	ECOD (v294.1)
C	7kD_DNA_binding	e1w4rC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: 7kD_DNA_binding	ECOD (v294.1)
D	7kD_DNA_binding	e1w4rD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: 7kD_DNA_binding	ECOD (v294.1)
E	7kD_DNA_binding	e1w4rE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: 7kD_DNA_binding	ECOD (v294.1)
F	7kD_DNA_binding	e1w4rF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: 7kD_DNA_binding	ECOD (v294.1)
H	7kD_DNA_binding	e1w4rH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: 7kD_DNA_binding	ECOD (v294.1)
G	7kD_DNA_binding	e1w4rG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: 7kD_DNA_binding	ECOD (v294.1)
A	NikR_C	e1w4rA3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: NikR_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
H	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
H	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
G	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	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	PF00265	Thymidine kinase (TK)	Thymidine kinase	-	Family

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	THYMIDINE KINASE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding thymidine kinase activity nucleobase-containing compound kinase activity deoxynucleoside kinase activity kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding transition metal ion binding zinc ion binding metal ion binding identical protein binding protein binding	deoxyribonucleoside metabolic process carbohydrate derivative metabolic process deoxyribonucleoside biosynthetic process nucleoside biosynthetic process pyrimidine nucleoside metabolic process nucleobase-containing compound metabolic process thymidine biosynthetic process nucleobase-containing small molecule metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process carbohydrate derivative biosynthetic process pyrimidine-containing compound metabolic process glycosyl compound biosynthetic process small molecule biosynthetic process deoxyribonucleoside metabolic process carbohydrate derivative metabolic process deoxyribonucleoside biosynthetic process nucleoside biosynthetic process pyrimidine nucleoside metabolic process nucleobase-containing compound metabolic process thymidine biosynthetic process nucleobase-containing small molecule metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process carbohydrate derivative biosynthetic process pyrimidine-containing compound metabolic process glycosyl compound biosynthetic process small molecule biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleoside metabolic process nucleobase-containing small molecule biosynthetic process pyrimidine deoxyribonucleoside biosynthetic process biosynthetic process pyrimidine nucleoside biosynthetic process metabolic process cellular process thymidine metabolic process pyrimidine deoxyribonucleoside metabolic process mitotic DNA replication DNA synthesis involved in mitotic DNA replication nuclear DNA replication cell cycle DNA replication mitotic cell cycle nucleic acid biosynthetic process cell cycle cell cycle process DNA-templated DNA replication DNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process DNA synthesis involved in DNA replication DNA replication mitotic cell cycle process macromolecule metabolic process DNA biosynthetic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol 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	IPR020633	Thymidine kinase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001267	Thymidine kinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	Pharos: P04183	Liver Neoplasms, Experimental lung adenocarcinoma colorectal cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor breast fibroadenoma endometriosis invasive ductal breast carcinoma osteosarcoma psoriasis adrenal cortex carcinoma breast cancer large cell medulloblastoma medulloblastoma Liver Neoplasms, Experimental lung adenocarcinoma colorectal cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor breast fibroadenoma endometriosis invasive ductal breast carcinoma osteosarcoma psoriasis adrenal cortex carcinoma breast cancer large cell medulloblastoma medulloblastoma ovarian cancer ulcerative colitis atopic eczema breast carcinoma colorectal carcinoma ductal breast carcinoma in situ hepatocellular carcinoma interstitial cystitis

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.