Structure of PDB 3dmg Chain A Binding Site BS01

Receptor Information
>3dmg Chain A (length=371) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTREAYHRLTPLPHPGGRLFIKPGARGYRDPVHDLLQKTVEPFGERALDL
NPGVGWGSLPLEGRMAVERLETSRAAFRCLTASGLQARLALPWEAAAGAY
DLVVLALPAGRGTAYVQASLVAAARALRMGGRLYLAGDKNKGFERYFKEA
RALLGYGVVVRREGPYRVALLEKEKEAPPLPSLWRAFSARILGAEYTFHH
LPGVFSAGKVDPASLLLLEALQERLGPEGVRGRQVLDLGAGYGALTLPLA
RMGAEVVGVEDDLASVLSLQKGLEANALKAQALHSDVDEALTEEARFDII
VTNPPFHVGGAVILDVAQAFVNVAAARLRPGGVFFLVSNPFLKYEPLLEE
KFGAFQTLKVAEYKVLFAEKR
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 chain3dmg Chain A Residue 388 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dmg Crystal Structure of the Thermus thermophilus 16 S rRNA Methyltransferase RsmC in Complex with Cofactor and Substrate Guanosine.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		F207 S216 G241 A242 A246 E262 D263 S287 V289 N305 V318 F322
Binding residue
(residue number reindexed from 1)		F205 S214 G239 A240 A244 E260 D261 S285 V287 N303 V316 F320
Annotation score4
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity
GO:0003676 nucleic acid binding
GO:0008168 methyltransferase activity
GO:0008170 N-methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
Biological Process
GO:0000154 rRNA modification
GO:0008033 tRNA processing
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0043414 macromolecule methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dmg, PDBe:3dmg, PDBj:3dmg
PDBsum3dmg
PubMed18667428
UniProtQ5SKW0

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