Structure of PDB 8cxw Chain A Binding Site BS01

Receptor Information

>8cxw Chain A (length=543) Species: 272563 (Clostridioides difficile 630)

YYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILYDL
FEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSLTN
KKDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKKYKKFLLE
KYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLSGKDLREY
IKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDVFKIKNED
ICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFYNKIQEKC
KYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWIKSKNINK
YIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRECKSGIRKW
YELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYSFFIKEEY
LDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMKIRIFRDN
NYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI

Ligand information

>8cxw Chain D (length=14)

ttcaaaaagtccca

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cxw Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
• Resolution: 2.78 Å
• Binding residue (original residue number in PDB): Y30 N165 Y168 K173 K193 Y221 S227 F253 G257 S344 F345 Q346 W439 R441 K456 Y476 K511 M513 S514 Y521 P522 N523
• Binding residue (residue number reindexed from 1): Y1 N131 Y134 K139 K159 Y187 S193 F219 G223 S310 F311 Q312 W405 R407 K422 Y442 K477 M479 S480 Y487 P488 N489

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:8cxw, PDBe:8cxw, PDBj:8cxw
• PDBsum: 8cxw
• PubMed: 36581322
• UniProt: Q183J3