Structure of PDB 8c58 Chain A Binding Site BS03

Receptor Information
>8c58 Chain A (length=376) Species: 272633 (Malacoplasma penetrans HF-2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIKVIKVFEAFAGIGSQFKALKNIARSKNWEIQHSGMVEWFVDAIVSYVA
IHSKNFNPKIERLDRDILSISNDSKMPISEYGIKKINNTIKASYLNYAKK
HFNNLFDIKKVNKDNFPKNIDIFTYSFPCQDLSVQTRSGLLWEIERILEE
IKNSFSKEEMPKYLLMENVKNLLSHKNKKNYNTWLKQLEKFGYKSKTYLL
NSKNFDNCQNRERVFCLSIRDDYLEKTGFKFKELEKVKNPPKKIKDILVD
SSNYKYLNLNKYETTTFRETKSNIISRPLKNYTTFNSENYVYNINGIGPT
LTASGANSRIKIETQQGVRYLTPLECFKYMQFDVNDFKKVQSTNLISENK
MIYIAGNSIPVKILEAIFNTLEFVNN
Ligand information
Ligand IDSAM
InChIInChI=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
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[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 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[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
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain8c58 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8c58 CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		F17 A18 G19 I20 S22 Q23 E45 W46 F112 D113 N374 S375
Binding residue
(residue number reindexed from 1)		F11 A12 G13 I14 S16 Q17 E39 W40 F106 D107 N357 S358
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.37: DNA (cytosine-5-)-methyltransferase.
Gene Ontology
Molecular Function
GO:0003886 DNA (cytosine-5-)-methyltransferase activity
GO:0008168 methyltransferase activity
Biological Process
GO:0009307 DNA restriction-modification system
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8c58, PDBe:8c58, PDBj:8c58
PDBsum8c58
PubMed38966999
UniProtQ8EVR5

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