Structure of PDB 4dkj Chain A Binding Site BS03

Receptor Information
>4dkj Chain A (length=388) Species: 272633 (Malacoplasma penetrans HF-2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKIKVIKVFEAFAGIGSQFKALKNIARSKNWEIQHSGMVEWFVDAIVSYV
AIHSKNFNPKIERLDRDILSISNDSKMPISEYGIKKINNTIKASYLNYAK
KHFNNLFDIKKVNKDNFPKNIDIFTYSFPCQDLSVQGLQKGIDKELNTRS
GLLWEIERILEEIKNSFSKEEMPKYLLMENVKNLLSHKNKKNYNTWLKQL
EKFGYKSKTYLLNSKNFDNCQNRERVFCLSIRDDYLEKTGFKFKELEKVK
NPPKKIKDILVDSSNYKYLNLNKYETTTFRETKSNIISRPLKNYTTFNSE
NYVYNINGIGPTLTASGANSRIKIETQQGVRYLTPLECFKYMQFDVNDFK
KVQSTNLISENKMIYIAGNSIPVKILEAIFNTLEFVNN
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain4dkj Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4dkj CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		F17 A18 G19 I20 S22 E45 W46 F112 D113 S132 R154 N374 S375
Binding residue
(residue number reindexed from 1)		F12 A13 G14 I15 S17 E40 W41 F107 D108 S127 R149 N369 S370
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) C135 E184 R228 R230
Catalytic site (residue number reindexed from 1) C130 E179 R223 R225
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:4dkj, PDBe:4dkj, PDBj:4dkj
PDBsum4dkj
PubMed23248272
UniProtQ8EVR5

[Back to BioLiP]