Structure of PDB 5by6 Chain B

Receptor sequence

>5by6B (length=288) Species: 6334 (Trichinella spiralis)

DYVNQEELNYLNQLKDIIDHGVRKNDRTGIGTLSTFGTQSRYCLRDDIFP
LLTTKRVFWRGVVEELLWFISGSTNAKQLSEKNVNIWDGNSSREFLDSRG
LYNYEEGDLGPVYGFQWRHFGCPYSSMTADYKGKGYDQLQQCIKMIREEP
ESRRIIMTAWNPCDLEKVALPPCHCFVQFYVADGELSCQMYQRSADMGLG
VPFNIASYSLLTRMIAHITSLKPGFFIHTIGDAHVYLTHVDALKVQMERK
PRPFPKLKILRNVENIDDFRAEDFELINYKPYPKISMP

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: B
• 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): E65 W87 Y113 C173 R193 D196
• 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	B	R169 R170	R153 R154
BS02	UMP	B	R43 C189 Q208 R209 S210 D212 N220 H250 Y252	R27 C173 Q192 R193 S194 D196 N204 H234 Y236

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