6PF3 | pdb_00006pf3

Crystal structure of human thymidylate synthase Delta (7-29) in complex with dUMP and 2-(4-((2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl)benzamido)-4-chlorobenzoic acid

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)
D	d6pf3d_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6pf3c_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6pf3b_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6pf3a_	Alpha and beta proteins (a+b)	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase/dCMP hydroxymethylase	Thymidylate synthase	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)
D	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8036156	3000544	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8036156	3000544	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8036156	3000544	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thymidylate synthase/dCMP hydroxymethylase	8036156	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)
D	Cas9_PI2	e6pf3D1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Cas9_PI2	ECOD (develop294)
C	Cas9_PI2	e6pf3C1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Cas9_PI2	ECOD (develop294)
B	Cas9_PI2	e6pf3B1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Cas9_PI2	ECOD (develop294)
A	AcrIIA6	e6pf3A1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: AcrIIA6	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	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	Thymidylate synthase	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity thymidylate synthase activity 5,10-methylenetetrahydrofolate-dependent methyltransferase activity catalytic activity vitamin binding organic acid binding binding ion binding modified amino acid binding folic acid binding anion binding carboxylic acid binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity thymidylate synthase activity 5,10-methylenetetrahydrofolate-dependent methyltransferase activity catalytic activity vitamin binding organic acid binding binding ion binding modified amino acid binding folic acid binding anion binding carboxylic acid binding heterocyclic compound binding small molecule binding translation regulator activity mRNA regulatory element binding translation repressor activity translation repressor activity RNA binding sequence-specific mRNA binding nucleic acid binding mRNA binding	primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process regulation of cellular process negative regulation of biological process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression translation regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of 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 deoxyribonucleotide biosynthetic process deoxyribonucleotide 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 nucleotide metabolic process nucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process methylation folic acid-containing compound metabolic process tetrahydrofolate interconversion modified amino acid metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process one-carbon metabolic 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	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036926	Thymidylate synthase/dCMP hydroxymethylase superfamily	Homologous Superfamily
A, B, C, D	IPR000398	Thymidylate synthase	Family
A, B, C, D	IPR045097	Thymidylate synthase/dCMP hydroxymethylase	Family
A, B, C, D	IPR020940	Thymidylate synthase, active site	Active Site
A, B, C, D	IPR023451	Thymidylate synthase/dCMP hydroxymethylase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P04818	malignant colon neoplasm breast carcinoma cleft palate squamous cell carcinoma follicular lymphoma colorectal cancer lung adenocarcinoma nervous system disorder non-small cell lung carcinoma gastric cancer head and neck cancer breast cancer Hyperammonemia malignant pancreatic neoplasm neuroendocrine neoplasm malignant colon neoplasm breast carcinoma cleft palate squamous cell carcinoma follicular lymphoma colorectal cancer lung adenocarcinoma nervous system disorder non-small cell lung carcinoma gastric cancer head and neck cancer breast cancer Hyperammonemia malignant pancreatic neoplasm neuroendocrine neoplasm ovarian cancer anemia rectal neoplasm brain disease prostate cancer medulloblastoma Sjogren syndrome nasopharyngeal carcinoma cystic fibrosis superficial multifocal basal cell carcinoma digestive system disease Down syndrome actinic keratosis pancreatic adenocarcinoma ductal breast carcinoma in situ pancreatic neoplasm atypical teratoid rhabdoid tumor pituitary cancer primitive neuroectodermal tumor hepatocellular carcinoma cancer cleft lip rectal carcinoma invasive ductal breast carcinoma reticulum cell sarcoma colorectal carcinoma small intestine cancer lung benign neoplasm neoplasm of neck testicular germ cell tumor Tourette syndrome pancreatic intraductal papillary-mucinous carcinoma endometriosis Pick disease gastric neoplasm lymphoplasmacytic lymphoma benign colon neoplasm head and neck neoplasm malignant ependymoma progressive supranuclear palsy hereditary diffuse gastric adenocarcinoma psoriasis IgA glomerulonephritis malignant pleural mesothelioma large cell medulloblastoma colonic neoplasm sinusitis lung cancer digestive system cancer tongue cancer non-Hodgkin lymphoma tuberculosis ovarian neoplasm adrenal cortex carcinoma pancreatic intraductal papillary-mucinous neoplasm atopic eczema pilocytic astrocytoma glioblastoma lymphosarcoma malignant glioma breast fibroadenoma rectal cancer interstitial cystitis malignant tumor of neck liver cancer

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.