Structure of PDB 8c45 Chain B Binding Site BS01

Receptor Information

>8c45 Chain B (length=1214) Species: 568708 (Salmonella enterica subsp. enterica serovar Typhimurium str. D23580)

TNNIKKYAPQARNQFRDAVIQKLTTLGISADKKGNLQIADAELVGETMRY
GQYPKSTLTRRDRLVKRAREQGFDVLVEHCAYTWFNRLCAIRYMEIHGYL
DHGFHMLSHPDNPTGFEVLDHVPEVAEALLPEKKAQLVEMKLSGNQEAIY
RELLLAQCHALHRAMPFLFEAVDDEAELLLPDNLTRTDSILRGLVDGIPE
EDWQEVEVIGWLYQFYISEKKDAVIGKVVKSEDIPAATQLFTPNWIVQYL
VQNSVGRQWLQTYPDSPLKGKMDYYIEPAEQTPEVQAQLAAITPASIEPE
SIKVLDPACGSGHILIEVYNVLKNIYEERGYRARDIPQLILENNIFGLDI
DDRAAQLSGFALLMMARQDDRRIFTRDVRLNIVSLQESLHLDIAKLWQQL
NFHQQNDMFAENTALAHTDSAEYQLLMRTLKRFVNAKTLGSLIQVPQEEE
AELKAFLEALYRMEQEGDFQQKAAAKAFIPYIQQAWILAQRYDAVVANPP
YMGGKGMNSELKEFAKNNFPDSKADLFAMFMQNAFSLLKENGFNAQVNMQ
SWMFLSSYEALRNWLLDNKTFITMAHLGARAFGQISGEVVQTTAWVIKNQ
HSERYQPVFFRLIDGREEVKKSDLLLRKNIFDKFTQHDFKNIPGMPIAYW
IDLPSLLSFRHHKKLGEKIALKAGMSTGDNIKFQRYWYEVSIKKTLITNK
ESNTKIDIHNIKWFPCSSGGEYRKWYGNNEIVVNWENNGYEIRNFKFENG
KTRSAVRNDEYYFREGITWSKISQGNFCVRYRPKGFVFDDTGRCGFSNNK
NELLYAAGLMCTPVVNHYLSILAPTLSFTSGELASVPYPEIEDEIIELVT
NAIEIAKNDWDSQEQSWDYVCSPLLEHNSTQLLRNIYKQKINTNIKLVET
LLLIENTINNIFIDKLQLDKTIIKAVLQSEITLLCNPNYRYKNIQDHTDL
TNKYYTDITIDILSYIIGCMMGRYSLDREGLVYAHEGNKGFAELVAEDAY
KTFPADNDGILPLMDDEWFDDDVTSRVKEFVRTVWGEEHLQENLEFIAES
LCLYAIKPKKGESALDTIRRYLSTQFWKDHMKMYKKRPIYWLFSSGKEKA
FECLVYLHRYNDATLARMRTEYVVPLLARYQANIDRLNEQVDGASGGEAT
RLKRERDSLSKKFNELRSFDDRLRHYADMRISIDLDDGVKVNYGKFGDLL
ADVKAITGNAPEII

Ligand information

• Ligand ID: SAM
• InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
• InChIKey: MEFKEPWMEQBLKI-FCKMPRQPSA-N
• SMILES:
  CACTVS 3.341: C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.341: C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
  ACDLabs 10.04: [O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C15 H22 N6 O5 S
• Name: S-ADENOSYLMETHIONINE
• ChEMBL: CHEMBL1235831
• PDB chain: 8c45 Chain B Residue 1301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8c45 Phage defence protein
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): Y218 T243 L245 F246 T247 A313 C314 G315 H318 I319 D354 I355 G451 N509 P511
• Binding residue (residue number reindexed from 1): Y213 T238 L240 F241 T242 A308 C309 G310 H313 I314 D349 I350 G440 N498 P500
• Annotation score: 5

Gene Ontology

Molecular Function

• GO:0008168 methyltransferase activity
• GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity

Biological Process

• GO:0032259 methylation

External links

• PDB: RCSB:8c45, PDBe:8c45, PDBj:8c45
• PDBsum: 8c45
• PubMed: 39174540
• UniProt: A0A6C7IK61