6K7Q | pdb_00006k7q

Crystal structure of thymidylate synthase from shrimp

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	d6k7qp_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
O	d6k7qo_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
N	d6k7qn_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
M	d6k7qm_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
L	d6k7ql_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
K	d6k7qk_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
J	d6k7qj_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
I	d6k7qi_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
H	d6k7qh_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
G	d6k7qg_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
F	d6k7qf_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
E	d6k7qe_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
D	d6k7qd_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
C	d6k7qc_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
B	d6k7qb_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)
A	d6k7qa_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	automated matches	Whiteleg shrimp (Penaeus vannamei ) [TaxId: 6689 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8096810	3000544	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	C1-set	e6k7qP1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
O	C1-set	e6k7qO1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
N	C1-set	e6k7qN1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
M	C1-set	e6k7qM1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
L	C1-set	e6k7qL1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
K	C1-set	e6k7qK1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
J	C1-set	e6k7qJ1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
I	C1-set	e6k7qI1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
H	C1-set	e6k7qH1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
G	C1-set	e6k7qG1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
F	C1-set	e6k7qF1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
E	C1-set	e6k7qE1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
D	C1-set	e6k7qD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
C	C1-set	e6k7qC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
B	C1-set	e6k7qB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
A	C1-set	e6k7qA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
O	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
N	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
M	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
L	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
K	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
J	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
I	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
H	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
G	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
F	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
E	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
D	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
C	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
B	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)
A	3.30.572.10	Alpha Beta	2-Layer Sandwich	Thymidylate Synthase	Chain A	CATH (utative)

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	PF00303	Thymidylate synthase (Thymidylat_synt)	Thymidylate synthase	This is a family of proteins that are flavin-dependent thymidylate synthases.	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	Thymidylate synthase	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity thymidylate synthase activity 5,10-methylenetetrahydrofolate-dependent methyltransferase activity catalytic activity	methylation metabolic process cellular 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 dTMP metabolic process phosphate-containing compound metabolic process methylation metabolic process cellular 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 dTMP metabolic process phosphate-containing compound metabolic process deoxyribonucleoside monophosphate biosynthetic process dTMP biosynthetic process small molecule metabolic process pyrimidine deoxyribonucleoside monophosphate biosynthetic process pyrimidine-containing compound biosynthetic process nucleoside monophosphate metabolic process phosphorus 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 nucleotide metabolic process nucleobase-containing compound biosynthetic process nucleoside monophosphate biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine deoxyribonucleoside triphosphate biosynthetic process dTTP biosynthetic process pyrimidine deoxyribonucleoside triphosphate metabolic process pyrimidine nucleoside triphosphate biosynthetic process pyrimidine nucleoside triphosphate metabolic process dTTP metabolic process nucleoside triphosphate biosynthetic process nucleoside triphosphate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle mitochondrion organelle 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	IPR045097	Thymidylate synthase/dCMP hydroxymethylase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR020940	Thymidylate synthase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR036926	Thymidylate synthase/dCMP hydroxymethylase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR023451	Thymidylate synthase/dCMP hydroxymethylase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR000398	Thymidylate synthase	Family

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.