Structure of PDB 1yf3 Chain B Binding Site BS03

Receptor Information
>1yf3 Chain B (length=249) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLAND
IQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDP
LLLYVLHFHGFSNMIRINYKGNFTTPFGKRTINKNSEKRFNHFKQNCDKI
IFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSL
NDRGIKFGLSNVLEHHGKENTLLKEWSKKYNVKHLNKKKNGTDEVYIFN
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 chain1yf3 Chain B 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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PDB1yf3 Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase.
Resolution2.29 Å
Binding residue
(original residue number in PDB)		Y7 N10 F32 C33 G35 S37 D50 I51 Q52 H156 F157 D171 P173 Y181 F184
Binding residue
(residue number reindexed from 1)		Y7 N10 F32 C33 G35 S37 D50 I51 Q52 H156 F157 D171 P173 Y181 F184
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:0008168 methyltransferase activity
GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity
GO:0009008 DNA-methyltransferase activity
GO:0043565 sequence-specific DNA binding
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0006260 DNA replication
GO:0006298 mismatch repair
GO:0009307 DNA restriction-modification system
GO:0019049 virus-mediated perturbation of host defense response
GO:0032259 methylation
GO:0052170 symbiont-mediated suppression of host innate immune response
GO:0099018 symbiont-mediated evasion of host restriction-modification system

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1yf3, PDBe:1yf3, PDBj:1yf3
PDBsum1yf3
PubMed15882618
UniProtP04392|DMA_BPT4 DNA adenine methylase (Gene Name=DAM)

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