Structure of PDB 8cxx Chain A Binding Site BS01

Receptor Information

>8cxx Chain A (length=546) Species: 272563 (Clostridioides difficile 630)

GIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILY
DLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSL
TNKKVDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKKYKKF
LLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLSGKDL
REYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDVFKIK
NEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFYNKIQ
EKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWIKSKN
INKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRECKSGI
RKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYSFFIK
EEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMKIRIF
RDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI

Ligand information

>8cxx Chain D (length=14)

ttcaaaaagtccca

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cxx 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 K173 K193 Y221 S227 F253 I256 G257 Q346 W439 R441 K456 Y476 K511 M513 S514 Y521 N523
• Binding residue (residue number reindexed from 1): Y3 N134 Y137 K142 K162 Y190 S196 F222 I225 G226 Q315 W408 R410 K425 Y445 K480 M482 S483 Y490 N492

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