Structure of PDB 8cy4 Chain B Binding Site BS01

Receptor Information

>8cy4 Chain B (length=550) Species: 1496 (Clostridioides difficile)

GIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILY
DLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSL
TNKKVVNDLDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKK
YKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLS
GKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDV
FKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFY
NKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWI
KSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRREC
KSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYS
FFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMK
IRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI

Ligand information

>8cy4 Chain F (length=14)

ttcaaaaagtccca

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cy4 Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
• Resolution: 2.34 Å
• Binding residue (original residue number in PDB): Y30 N165 Y168 H171 K173 K193 Y221 S227 I256 G257 Q346 R432 W439 R441 K456 Y476 K511 M513 S514 Y521 P522 N523
• Binding residue (residue number reindexed from 1): Y3 N138 Y141 H144 K146 K166 Y194 S200 I229 G230 Q319 R405 W412 R414 K429 Y449 K484 M486 S487 Y494 P495 N496

Enzymatic activity

• Enzyme Commision number: 2.1.1.72: site-specific DNA-methyltransferase (adenine-specific).

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0008168 methyltransferase activity
• GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity

Biological Process

• GO:0006304 DNA modification
• GO:0032259 methylation

External links

• PDB: RCSB:8cy4, PDBe:8cy4, PDBj:8cy4
• PDBsum: 8cy4
• PubMed: 36581322
• UniProt: Q183J3