Structure of PDB 5by6 Chain C

Receptor sequence

>5by6C (length=286) Species: 6334 (Trichinella spiralis)

YVNQEELNYLNQLKDIIDHGVRKNDRTGIGTLSTFGTQSRYCLRDDIFPL
LTTKRVFWRGVVEELLWFISGSTNAKQLSEKNVNIWDGNSSREFLDSRGL
YNYEEGDLGPVYGFQWRHFGCPYSSMTADYKGKGYDQLQQCIKMIREEPE
SRRIIMTAWNPCDLEKVALPPCHCFVQFYVADGELSCQMYQRSADMGLGV
PFNIASYSLLTRMIAHITSLKPGFFIHTIGDAHVYLTHVDALKVQMERKP
RPFPKLKILRNVENIDDFRAEDFELINYKPYPKISM

3D structure

• PDB: 5by6 Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS.
• Chain: C
• Resolution: 1.9 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E81 W103 Y129 C189 R209 D212
• Catalytic site (residue number reindexed from 1): E64 W86 Y112 C172 R192 D195
• Enzyme Commision number: 2.1.1.45: thymidylate synthase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	UMP	C	R43 C189 Q208 R209 S210 D212 N220 H250 Y252	R26 C172 Q191 R192 S193 D195 N203 H233 Y235
BS02	UMP	C	R169 R170	R152 R153

Gene Ontology

Molecular Function

• GO:0004799 thymidylate synthase activity
• GO:0008168 methyltransferase activity
• GO:0016741 transferase activity, transferring one-carbon groups

Biological Process

• GO:0006231 dTMP biosynthetic process
• GO:0006235 dTTP biosynthetic process
• GO:0009165 nucleotide biosynthetic process
• GO:0032259 methylation

Cellular Component

• GO:0005739 mitochondrion
• GO:0005829 cytosol

External links

• PDB: RCSB:5by6, PDBe:5by6, PDBj:5by6
• PDBsum: 5by6
• PubMed: 28826032
• UniProt: Q9NDD3