Structure of PDB 4rtr Chain A Binding Site BS02

Receptor Information
>4rtr Chain A (length=244) Species: 1110693 (Escherichia coli str. K-12 substr. MDS42) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYIL
ADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQ
DPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFA
EKAQNAFFYCESYADSMARADDSSVVYCDPPYAPLSFTLEQQAHLAEIAE
GLVERHIPVLISNHDTMLTREWYQRAKLHVVKVDELLALYKPGV
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 chain4rtr Chain A Residue 301 [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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PDB4rtr Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression.
Resolution2.393 Å
Binding residue
(original residue number in PDB)		W10 A11 G12 F35 D54 I55 S164 Y165 D181 P182 P183 Y184
Binding residue
(residue number reindexed from 1)		W8 A9 G10 F33 D52 I53 S162 Y163 D179 P180 P181 Y182
Annotation score5
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:0003677 DNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity
GO:0043565 sequence-specific DNA binding
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006298 mismatch repair
GO:0009307 DNA restriction-modification system
GO:0009411 response to UV
GO:0032259 methylation
GO:1902328 bacterial-type DNA replication initiation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4rtr, PDBe:4rtr, PDBj:4rtr
PDBsum4rtr
PubMed25845600
UniProtP0AEE8|DMA_ECOLI DNA adenine methylase (Gene Name=dam)

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