Structure of PDB 5ybb Chain A Binding Site BS01

Receptor Information
>5ybb Chain A (length=487) Species: 273068 (Caldanaerobacter subterraneus subsp. tengcongensis MB4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQTRESLANEIWRACDIMRRDNNCTGIMEYVEHLAWLLFLRFLDAQEEEW
EAQAQIPIIDSEYRWRHWATKDWPADELLAFVHGRLIPYLRSLGGDPLRE
TIRSLFSERNVIVCASGYNLKDVIQIVNEINFHSQDDIFTVSQVYEELLR
RLGNENRLAGEFYTPRPVVRFVVELVDPQIGEAVYDPACGTCGFLVEAYL
WMKQKERTIEDHRILQERTFFGQEKKPVPAFLGLVNMMLHGVTVPRVMRR
NTLEENIRNVSERFDVVVTNPPFGGTEGRHIQQNFPIQSNATELLFLQHI
MKKLKPRDGARCGMVVPEGTLFRGGAFAEVKRDLLEQFNLHTVVSLPPGT
FAPYSDVKTALIFFERPGPTKEIWYYELPLPEGLKKFSKGNPIQDEHFEE
ARKLWRGWDAYRKGLGPVEACLSERSWIVPVEEVKKRGYDLTARNPNRSG
GEELPSPVEIVAGLLEKEREILSIMEELSELLENEKG
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 chain5ybb Chain A Residue 601 [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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PDB5ybb Structural basis underlying complex assembly and conformational transition of the type I R-M system.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		E170 F171 T173 A197 G199 G202 F203 E233 K234 N260 T261 N279 F305
Binding residue
(residue number reindexed from 1)		E161 F162 T164 A188 G190 G193 F194 E224 K225 N251 T252 N270 F296
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:0008170 N-methyltransferase activity
GO:0009007 site-specific DNA-methyltransferase (adenine-specific) 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:5ybb, PDBe:5ybb, PDBj:5ybb
PDBsum5ybb
PubMed28973912
UniProtQ8R9Q4

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