Structure of PDB 3eeo Chain A Binding Site BS03

Receptor Information
>3eeo Chain A (length=327) Species: 735 (Haemophilus parahaemolyticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYE
MNFGEKPEGDITQVNEKTIPDHDILCAGFPCQAFSISGKQKGFEDSRGTL
FFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAK
VLNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDS
EVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGERIYSTRGIAIT
LSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYK
QFGNSVVINVLQYIAYNIGSSLNFKPY
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 chain3eeo Chain A Residue 328 [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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PDB3eeo M. HhaI co-crystallized with synthetic dsDNA containing a propane diol in place of the deoxycytidine residue targeted for methylation.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		F18 G23 E40 W41 G78 N304 S305 V306
Binding residue
(residue number reindexed from 1)		F18 G23 E40 W41 G78 N304 S305 V306
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) C81 E119 R163 R165
Catalytic site (residue number reindexed from 1) C81 E119 R163 R165
Enzyme Commision number 2.1.1.37: DNA (cytosine-5-)-methyltransferase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
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
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Biological Process
External links
PDB RCSB:3eeo, PDBe:3eeo, PDBj:3eeo
PDBsum3eeo
PubMed
UniProtP05102|MTH1_HAEPH Type II methyltransferase M.HhaI (Gene Name=hhaIM)

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